Tag: RSQLite

Administration Guide – R Package Dependencies

The following is a list of all of the R packages RStudio depends on in some way. None of these packages are necessary for the basic operation of RStudio; they all enable additional IDE functionality as noted in in Features. This information is also available in the IDE itself using…

Continue Reading Administration Guide – R Package Dependencies

r – Support of nanotime by RSQLite

I am looking into what is required to support nanotime objects in RSQLite queries. They are just integer64 wrappers. Here is an example: con <- DBI::dbConnect(RSQLite::SQLite(), “:memory:”) ts <- nanotime::as.nanotime(Sys.time()) str(ts) # integer64 2023-06-04 17:30:21.669581000 DBI::dbGetQuery(con, ‘SELECT :ts AS x’, list(‘ts’ = ts)) # returns 5.757609e-196 tsi <- bit64::as.integer64(ts) DBI::dbGetQuery(con,…

Continue Reading r – Support of nanotime by RSQLite

lfcshrink error DESeq2

Hello! I’m having problems with lfcShrink in my DESeq2 workflow. I’m trying to do a differential expression analysis (with only one comparison term: “MULTIseq_ID_call2”) on my single-cell data. However when I do lfcShrink I get an error that I cannot interpret. Can you help me? dds <- DESeq(dds, test =…

Continue Reading lfcshrink error DESeq2

Bioconductor – MsBackendSql

DOI: 10.18129/B9.bioc.MsBackendSql   SQL-based Mass Spectrometry Data Backend Bioconductor version: Release (3.17) SQL-based mass spectrometry (MS) data backend supporting also storange and handling of very large data sets. Objects from this package are supposed to be used with the Spectra Bioconductor package. Through the MsBackendSql with its minimal memory footprint,…

Continue Reading Bioconductor – MsBackendSql

C R Package Dependencies | RStudio Server Professional Edition 1.3.937-3

base64enc 0.1-3 R Markdown crayon 1.3.4 Plumber R APIs, Shiny curl 4.2 Publishing DBI 0.8 Database Interface, RSQLite devtools 1.11.1 R Unit Testing digest 0.6 R Markdown, Shiny evaluate 0.13 R Markdown glue 1.3.0 R Markdown haven 0.2.0 SPSS/SAS/Stata Import highr 0.3 R Markdown htmltools 0.3.6 R2D3, R Markdown, Shiny,…

Continue Reading C R Package Dependencies | RStudio Server Professional Edition 1.3.937-3

Bioconductor – pd.2006.07.18.mm8.refseq.promoter

    This package is for version 2.11 of Bioconductor; for the stable, up-to-date release version, see pd.2006.07.18.mm8.refseq.promoter. Platform Design Info for NimbleGen 2006-07-18_mm8_refseq_promoter Bioconductor version: 2.11 Platform Design Info for NimbleGen 2006-07-18_mm8_refseq_promoter Author: Martin Aryee Maintainer: Martin Aryee <aryee at jhu.edu> Citation (from within R, enter citation(“pd.2006.07.18.mm8.refseq.promoter”)): Installation To…

Continue Reading Bioconductor – pd.2006.07.18.mm8.refseq.promoter

Bioconductor – synaptome.db (development version)

DOI: 10.18129/B9.bioc.synaptome.db   This is the development version of synaptome.db; for the stable release version, see synaptome.db. Synamptosome Proteome Database Bioconductor version: Development (3.17) The package contains local copy of the Synaptic proteome database. On top of this it provide a set of utility R functions to query and analyse…

Continue Reading Bioconductor – synaptome.db (development version)

Gene duplicate

Gene duplicate 1 Hi there, I am pretty new to single cell RNA seq and I am trying to learn by doing analysis for a data that has been published already. I am using monocle3 and I realized that some Ensembl IDs that are the same and I was wondering…

Continue Reading Gene duplicate

Error generating counts df for use with DRIMSeq/DEXseq

Hi, I am attempting to work through the workflow described in “Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification.” I am running into an error message when I try to make the counts dataframe for DRIMseq: Error in data.frame(gene_id = txdf$GENEID, feature_id = txdf$TXNAME, cts) : arguments…

Continue Reading Error generating counts df for use with DRIMSeq/DEXseq

TxDB.Hsapiens.UCSC.hg38.knownGene with locateVariants() identifying SNPs from various chromosome being part of the same gene

I am trying to annotate a list of SNPs using the hg38 genome (knownGene) and locateVariants(). The program is able to successfully run and provide “GeneIDs” for several of the loci. However, some GeneIDs are applied to SNPs in completely different regions and on completely different chromosomes. When I cross…

Continue Reading TxDB.Hsapiens.UCSC.hg38.knownGene with locateVariants() identifying SNPs from various chromosome being part of the same gene

merge (all=T) error – rstudio

I have two installations of RStudio with each different updates of the packages. On the recent packages I get two errors that I don’t have with the previous packages. Can someone tell me what the problem is? Error 1: df_lofreq_3_DEL <- merge(df_lofreq_3_DEL, deletions_VAR_df_sub_freq, by.x=”VAR_MUT”, by.y=”lofreq_del”, all=T) Error in if (all.x)…

Continue Reading merge (all=T) error – rstudio

DESeq2: invalid class “GRangesList” object

Hi all, I am not sure if this is the right place to ask this question, but I’ve just updated my DESeq2 package from version 1.4.5 to version 1.6.3 and my scripts are no longer working. Specifically, I get the following error when generating a DESeqDataSet object with the function…

Continue Reading DESeq2: invalid class “GRangesList” object

[bullseye] r-cran-ggplot2 depends on missing libpq5 v13.8

Hi, I am on bullseye and am trying to install the package r-cran-ggplot2. This fails with E: Failed to fetch deb.debian.org/debian/pool/main/p/postgresql-13/libpq5_13.8-0%2bdeb11u1_amd64.deb 404 Not Found [IP: 146.75.122.132 80] (full output below). There seems to be a dependency on libpq5 version 13.8 whereas the version available for bullseye is 13.9. Any ideas how to…

Continue Reading [bullseye] r-cran-ggplot2 depends on missing libpq5 v13.8

Bioconductor – ChemmineR

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see ChemmineR. Cheminformatics Toolkit for R Bioconductor version: 2.13 ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of…

Continue Reading Bioconductor – ChemmineR

HTSeqGenie run error

Hi, I am running the HTSeqGenie on both MacOS and Linux with the test TP53 samples. They both gave me error in reading the fastq files. It seems having problems reading the fastq.gz files in each parallel process. Could anyone help me with this please? Error are at below: checkConfig.R/checkConfig.template:…

Continue Reading HTSeqGenie run error

Potential problem with independent filtering in DESeq2

Potential problem with independent filtering in DESeq2 1 @8a6e6497 Last seen 16 hours ago United States Hello, I was routinely using DESeq2 for some small RNA-seq datasets, and suddenly I noticed that FDR corrections are too aggressive. After some investigation, I found out that independent filtering is wrongly determining the…

Continue Reading Potential problem with independent filtering in DESeq2

RSQLite package – RDocumentation

Embeds the SQLite database engine in R, providing a DBI-compliant interface. SQLite is a public-domain, single-user, very light-weight database engine that implements a decent subset of the SQL 92 standard, including the core table creation, updating, insertion, and selection operations, plus transaction management. You can install the latest released version…

Continue Reading RSQLite package – RDocumentation

Strange Cook’s Values with DESeq2

Hi, I’m currently trying to assess fold change when comparing two different sample types using DESeq2 package and I’m getting weird Cook’s distance values which are causing major problems. The two different samples have different amounts of replicates (6 replicates vs 5 replicates) which might be the reason for these…

Continue Reading Strange Cook’s Values with DESeq2

Bioconductor – metaseqR2

DOI: 10.18129/B9.bioc.metaseqR2     An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms Bioconductor version: Release (3.11) Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining…

Continue Reading Bioconductor – metaseqR2

Unable to install clusterProfiler on Mac M1

Hi, I failed to install clusterProfiler on Mac M1. May I ask the solution >BiocManager::install(“clusterProfiler”) Bioconductor version 3.14 (BiocManager 1.30.19), R 4.1.3 (2022-03-10) Installing package(s) ‘clusterProfiler’ also installing the dependencies ‘fgsea’, ‘DOSE’, ‘enrichplot’, ‘GOSemSim’ Warning: unable to access index for repository bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1: cannot open URL ‘https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES’ Warning: unable to access…

Continue Reading Unable to install clusterProfiler on Mac M1

getTable ignores query ranges

HI everyone. I have a set of mouse SNPs (~974) from GRCm39 that I’m trying to get either GERP or UCSC Conservation scores on. To do this, I’m using rtracklayer to try to query the ranges of the SNP and return the multiz35way conservation score. However, when I do this,…

Continue Reading getTable ignores query ranges

microRNAs not available in TxDb.Hsapiens.UCSC.hg38.knownGene

microRNAs not available in TxDb.Hsapiens.UCSC.hg38.knownGene 0 @lluis-revilla-sancho Last seen 8 hours ago European Union I was looking to some examples and I could retrieve the microRNAs of the hg19 transcriptome, but not from the hg38 transcript annotation. I realized this might be because TxDb.Hsapiens.UCSC.hg38.knownGene doesn’t have a miRBase build ID,…

Continue Reading microRNAs not available in TxDb.Hsapiens.UCSC.hg38.knownGene

Error printing a CompressedGRangesList

I’m trying to annotate some data from a Bisulphite experiment, from which I have a GRanges object without any annotation: GRanges object with 872900 ranges and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> <Rle> [1] chr10 48196 * [2] chr10 48486 * [3] chr10 49247 * [4] chr10 49258…

Continue Reading Error printing a CompressedGRangesList

Error in UseMethod(“rescale”)

Error in UseMethod(“rescale”) 0 @2528ae94 Last seen 17 hours ago United States While using cnetplot to plot enrichGo results, I am getting the following error. It used to work before, but now I am constantly getting this error. I am using clusterprofiler package gse <- enrichGO(gene = deGenes, ont =…

Continue Reading Error in UseMethod(“rescale”)

r – Cannot Install maftools into BiocManager due to RSQLite

I am a relatively new R-user. I am currently working on trying to read .maf files via the maftools package released by Bioconductor. I am following the instructions as posted on the Bioconductor website (www.bioconductor.org/packages/devel/bioc/vignettes/maftools/inst/doc/maftools.html#4_Installation), however, everytime I attempt to run the installation, it gets stuck on RSQLite and I…

Continue Reading r – Cannot Install maftools into BiocManager due to RSQLite

lazy loading failed, unable to load shared object rtracklayer.so

Hello! I am working on analyzing a dataset I created with the 10x Chromium Single Cell Multiome kit. In order to add gene annotation to the ATAC data, I am trying to install and use the “EnsDb.Mmusculus.v79” and “BSgenome.Mmusculus.UCSC.mm10” packages with bioconductor. The same ERROR has come up repeatedly whenever…

Continue Reading lazy loading failed, unable to load shared object rtracklayer.so

Log2FC values slightly higher in some genes after DESeq2 shrinkage

Hi, I have a question about DESeq2 LFCshrinkage: Is it possible that some genes have a slightly higher LFC after shrinkage? It happened during my RNAseq DE analysis, I have very deeply sequenced samples with large base means. I tried visualizing using MAplot check, and it looks fine. I’m mainly…

Continue Reading Log2FC values slightly higher in some genes after DESeq2 shrinkage

Bioconductor – lumi

DOI: 10.18129/B9.bioc.lumi     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see lumi. BeadArray Specific Methods for Illumina Methylation and Expression Microarrays Bioconductor version: 3.12 The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina…

Continue Reading Bioconductor – lumi

[BioC] rtracklayer 1.6: invalid class “ucscCart” object

Dear Bioc, Following the rtracklayer documentation, section 2.2.4, ‘A Shortcut’, I encounter the following error browseGenome (subTargetTrack) Error in validObject(.Object) :invalid class “ucscCart” object: superclass “ANYTHING” not defined in the environment of the object’s class traceback () 13: stop(msg, ” “, errors, domain = NA)12: validObject(.Object)11: initialize(value, …)10: initialize(value, …)9:…

Continue Reading [BioC] rtracklayer 1.6: invalid class “ucscCart” object

Error in SummarizedExperiment

I have installed DESeq2 version 1.36.0 samples <- colnames(txi$counts) group <- as.factor(c(“control”,”control”,”control”,”control”,”control”,”diet”,”diet”,”diet”,”diet”,”diet”, “control”,”control”,”control”,”control”,”control”,”diet”,”diet”,”diet”,”diet”,”diet”,”diet”)) coldata <- data.frame(samples, group, stringsAsFactors = F) coldata <- coldata[,c(“samples”,”group”)] coldata$samples <- factor(coldata$samples) coldata$group <- factor(coldata$group) rownames(coldata) <- sub(“fb”, “”, rownames(coldata)) all(rownames(coldata$samples) %in% colnames(txi)) all(rownames(coldata) == colnames(txi)) TRUE library(DESeq2) ddsTxi <- DESeqDataSetFromTximport(txi, colData = coldata, design =…

Continue Reading Error in SummarizedExperiment

deseq2 problem

deseq2 problem 0 Hi I am trying to draw a PCA plot with DESeq2 but somehow I cannot use DESeq2 functions. It is a really simple code i wil be pasting below. > transform <- DESeq2::rlog(eliminated_data, blind = TRUE) Error in (function (classes, fdef, mtable) : unable to find an…

Continue Reading deseq2 problem

GDCprepare of RNAseq counts produces error

GDCprepare of RNAseq counts produces error 1 @76ac7b25 Last seen 12 minutes ago Canada Hello everyone! I have been using the TCGAbiolinks package for the last couple years to access RNAseq data for the TCGA-LAML project. Just very recently, I had noticed that I could no longer use GDCquery to…

Continue Reading GDCprepare of RNAseq counts produces error

Separate exogenous from endogenous transcripts using Salmon RNAseq DTU

Dear friends, We are trying to use Salmon for DTU analysis. We want to separate exogenous from endogenous transcripts by following this post www.biostars.org/p/443701/ and this paper f1000research.com/articles/7-952 We are focusing on a gene called ASCL1 (endo-ASCL1). We transduced cells with lentiviral vector containing ASCL1 ORF only (Lenti-ASCL1). There should…

Continue Reading Separate exogenous from endogenous transcripts using Salmon RNAseq DTU

GDCquery_Maf error

GDCquery_Maf error 0 @76e1237b Last seen 1 day ago Singapore Hi all, I really need some help. I am trying to run GDCquery_Maf which worked fine until yesterday. Now I get the following error: Error in GDCquery(paste0(“TCGA-“, tumor), data.category = “Simple Nucleotide Variation”, : Please set a valid workflow.type argument…

Continue Reading GDCquery_Maf error

subpopulations available in MafH5.gnomAD.v3.1.1.GRCh38

subpopulations available in MafH5.gnomAD.v3.1.1.GRCh38 1 @b14a6f0d Last seen 16 hours ago United States Are subpopulation MAFs available for gnomADv.3.1.1 with any package, like they are in MafDb.gnomAD.r2.1.hs37d5? I’m trying to use Genomic Scores to obtain all variants in a genomic range with MAF in any subpopulation >= cutoff. I tried…

Continue Reading subpopulations available in MafH5.gnomAD.v3.1.1.GRCh38

RSQLite: binding sets and scalars in the same select query

Why do you specify y = I(list(7,6)) instead of y=c(6,7)? This seems to work: dbGetQuery (c, “select * from tst where x = ? and y in (?)”, data.frame(x=1, y=c(7,6))) You might be looking for expand.grid. dbGetQuery (c, “select * from tst where x = ? and y in (?)”,…

Continue Reading RSQLite: binding sets and scalars in the same select query

Questions tagged rsqlite – DevDreamz

Python Javascript Linux FAQ LoginSignup PUBLIC All Questions Tags Snippets Jobs rsqlitersqlite rsqlitedata-tablesqliter rsqlitersqlite sqlrdatabasersqlite sqlrprepared-statementrsqlitedatabase rr-markdowndata-wranglingrsqlitesql rrsqlitesqlite rsqliter-dbir rsqlitersqlite sqldfrrsqlite PreviousNext Recent Posts show same id one time but in column count how many times php Assign bundle or argument to ImageView in Android ValueRequiredException during RSS feed parsing…

Continue Reading Questions tagged rsqlite – DevDreamz

Bioconductor installation problems

Dear Friends, I have been having considerable difficulty doing various package related bioconductor actions. Here is my system specifications: ======================================================================= macOS Monterey Version: 12.3 (21E230) MacBook Pro (Retina, 13-inch, Early 2015) Memory: 16 GB 1867 MHz DDR3 RStudio 2021.09.0 Build 351 R version 4.1.2 (2021-11-01) — “Bird Hippie” Copyright (C)…

Continue Reading Bioconductor installation problems

Bioconductor Package Installation

When I try to install the gtf for hg38 BiocManager::install(“TxDb.Hsapiens.UCSC.hg38.knownGene”) I get the following error: ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: cran.rstudio.com/ Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01) Installing package(s) ‘TxDb.Hsapiens.UCSC.hg38.knownGene’ Error in readRDS(dest) : error reading from connection Per stackoverflow.com/questions/67455984/getoptionrepos-replaces-bioconductor-standard-repositories-see-reposito I…

Continue Reading Bioconductor Package Installation

rsqlite database python (1) – Code Examples

python – OperationalError: database is locked I have made some repetitive operations in my application(testing it), and suddenly I’m getting a weird error: OperationalError: database is locked I’ve restarted the server, but the error persists.… how to close resultset in RMySQL? I…

Continue Reading rsqlite database python (1) – Code Examples

Pathway analysis of RNAseq data using goseq package

Hello, I have finished the RNA seq analysis and I am trying to perform some pathway analysis. I have used the gage package and I was looking online about another package called goseq that takes into account length bias. However, when I run the code I get an error. How…

Continue Reading Pathway analysis of RNAseq data using goseq package

Installation and set up of R6 rocker object

Installation of current released version from CRAN install.packages(“rocker”) Installation of current development version from GitHub install.packages(“devtools”) devtools::install_github(“nikolaus77/rocker”) Create new rocker database handling object Option 1 db <- rocker::newDB() # New database handling object #> dctr | New object Option 2 db <- rocker::rocker$new() # New database handling object #> dctr…

Continue Reading Installation and set up of R6 rocker object

DESeq2 and high prefiltering cutoff

DESeq2 and high prefiltering cutoff 1 @255004b1 Last seen 3 hours ago United States Hi, I am curious about prefiltering with DESeq2. I understand from this site and reading the DESeq2 vignette that prefiletering is really unnecessary as DESeq2 has a stringent filtering that it does. However, I’m seeing better…

Continue Reading DESeq2 and high prefiltering cutoff

Mixed Type: option to return list instead of coercing

I now think that the default mode should be to return an error here. That ship has sailed now. SQLite is fairly unique in its flexibility to store arbitrary data in the columns. For your use case I’d recommend segmenting by data type: library(RSQLite) con <- dbConnect(SQLite(), “:memory:”) dbGetQuery(con, “SELECT…

Continue Reading Mixed Type: option to return list instead of coercing

pmk21/rsqlite – gitmetadata

A simple SQLite clone in Rust. This is basically a translation of the C code present on this brilliant tutorial into Rust(not fully idiomatic). This code contains implementation only upto Part 5 in the tutorial. This a very simple database and is a small project I took up to gain…

Continue Reading pmk21/rsqlite – gitmetadata

traviz 1.0.0 installation fails: ERROR: lazy loading failed

Hi, I cannot install traviz package (version 1.0.0) from Bioconductor on a linux machine (from source). I have a conda environment, and I installed traviz from conda, but it cannot be used – when I do library(traviz) R just crashes and quits without any message. So I tried to install…

Continue Reading traviz 1.0.0 installation fails: ERROR: lazy loading failed

R connection to sqlite – Stackify

SQLite is a file level database, hence to reference it requires a full directory path. No where do you specify the working directory or a full path in the file name. By default, R will use the current working directory contained in getwd(). If database is not contained in this…

Continue Reading R connection to sqlite – Stackify

Having problem with RSQLite : RStudio

Hi, I’m trying to learn how to use RSQLite but I’m already having a problem, wondered if anyone knows how to fix it. I have a pre-existing database (.data) file which does not have attribute names and I am trying to create a SQLite database with a table defined with…

Continue Reading Having problem with RSQLite : RStudio

sqliteCopyDatabase function – RDocumentation

Description Copies a database connection to a file or to another database connection. It can be used to save an in-memory database (created using dbname = “:memory:” or dbname = “file::memory:”) to a file or to create an in-memory database a copy of another database. Usage sqliteCopyDatabase(from, to) Arguments from…

Continue Reading sqliteCopyDatabase function – RDocumentation

Accepted r-cran-rsqlite 2.2.9-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Wed, 29 Dec 2021 01:12:39 +0530 Source: r-cran-rsqlite Architecture: source Version: 2.2.9-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Nilesh Patra <nil…@debian.org> Changes: r-cran-rsqlite (2.2.9-1) unstable; urgency=medium . * Team Upload. [ Andreas Tille ] * Disable…

Continue Reading Accepted r-cran-rsqlite 2.2.9-1 (source) into unstable

How do I “flush” data to my RSQLite disk database?

You’re not using the pattern suggested by the RSQLite documentation. That documentation uses dbWriteTable to copy a data frame into a SQLite table: dbWriteTable(con, “mtcars”, mtcars) According to this documentation, your full code would look something like this: con <- dbConnect(RSQLite::SQLite(), “./mtcars.db”) data(mtcars) dbWriteTable(con, “mtcars”, mtcars) dbListTables(con) # Fetch all…

Continue Reading How do I “flush” data to my RSQLite disk database?

sqldf : create table from data frame error: “no such table”. and two tables created instead of one

UPDATE: newest versions of RSQLite and sqldf do not have the incompatibility issues addressed by this question i.e.: sqldf_0.4-10 RSQLite_1.1-2 work together well – Nathan All: Thanks to G. Grothendieck for pointers to incompatibility issues introduced by RSQLite 1.1-1. As stated in the comment to the answer, downgrade RSQLite to…

Continue Reading sqldf : create table from data frame error: “no such table”. and two tables created instead of one

identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE

GenomicFeatures::makeTxDbFromUCSC failing with an error: identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE 1 @mikhail-dozmorov-23744 Last seen 1 day ago United States Hi,The GenomicFeatures::makeTxDbFromUCSC function fails with: library(GenomicFeatures) > hg19.refseq.db <- makeTxDbFromUCSC(genome=”hg19″, table=”refGene”) Download the refGene table … Error in .fetch_UCSC_txtable(genome(session), tablename, transcript_ids = transcript_ids) : identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE OK The…

Continue Reading identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE

r – RSQLite Error “hash is not an exported object”

I am trying to scrape some pitchf/x data and store it in an SQLite database. However, I am receiving the following error when I run the following code: library(RSQLite) library(dplyr) db <- src_sqlite(“pitchfx.sqlite3”, create = T) This is the error: Error in h(simpleError(msg, call)) : error in evaluating the argument…

Continue Reading r – RSQLite Error “hash is not an exported object”

Design formula in DESeq2

Hello, I am using DESeq2 for analysis of RNAseq data. I would like to ask you about the design in the DESEq2 formula. I have tissue from animals treated with a chemical and my animal model is a colorectal cancer model. My variables are gender (male or female), treatment (treated…

Continue Reading Design formula in DESeq2

r – RSQlite – Find values with most occurences in group

I’m using RSQlite to import Datasets from an SQlite-Database. There are multiple millions of observations within the Database. Therefor I’d like to do as much as possible of Data selection and aggregation within the Database. At some point I need to aggregate a character variable. I want to get the…

Continue Reading r – RSQlite – Find values with most occurences in group

Bioconductor – pd.ht.hg.u133a

    This package is for version 2.14 of Bioconductor; for the stable, up-to-date release version, see pd.ht.hg.u133a. Platform Design Info for The Manufacturer’s Name HT_HG-U133A Bioconductor version: 2.14 Platform Design Info for The Manufacturer’s Name HT_HG-U133A Author: Benilton Carvalho Maintainer: Benilton Carvalho <beniltoncarvalho at gmail.com> Citation (from within R,…

Continue Reading Bioconductor – pd.ht.hg.u133a

Bioconductor – pd.hg.focus

    This package is for version 2.14 of Bioconductor; for the stable, up-to-date release version, see pd.hg.focus. Platform Design Info for The Manufacturer’s Name HG-Focus Bioconductor version: 2.14 Platform Design Info for The Manufacturer’s Name HG-Focus Author: Benilton Carvalho Maintainer: Benilton Carvalho <beniltoncarvalho at gmail.com> Citation (from within R,…

Continue Reading Bioconductor – pd.hg.focus

Bioconductor – pd.raex.1.0.st.v1

    This package is for version 2.14 of Bioconductor; for the stable, up-to-date release version, see pd.raex.1.0.st.v1. Platform Design Info for Affymetrix RaEx-1_0-st-v1 Bioconductor version: 2.14 Platform Design Info for Affymetrix RaEx-1_0-st-v1 Author: Benilton Carvalho Maintainer: Benilton Carvalho <Benilton.Carvalho at cancer.org.uk> Citation (from within R, enter citation(“pd.raex.1.0.st.v1”)): Installation To…

Continue Reading Bioconductor – pd.raex.1.0.st.v1

Outliers on DESEq2 Results

I have an RNAseq dataset, where one of the genes I intend to analyze has hundreds of counts ranging from 10 to 12, with a few counts > 9000. I process this data in Deseq2 and get that the gene is differentially expressed across several samples of interest. What can…

Continue Reading Outliers on DESEq2 Results

Bioconductor – pd.feinberg.mm8.me.hx1

    This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see pd.feinberg.mm8.me.hx1. Platform Design Info for NimbleGen feinberg_mm8_me_hx1 Bioconductor version: 2.8 Platform Design Info for NimbleGen feinberg_mm8_me_hx1 Author: Martin Aryee Maintainer: Martin Aryee <aryee at jhu.edu> Citation (from within R, enter citation(“pd.feinberg.mm8.me.hx1”)): Installation To…

Continue Reading Bioconductor – pd.feinberg.mm8.me.hx1

weird MAplot or volcano plot of DESeq2 diff result

Hi, every one. I find a werid MAplot or volcano plot of DESeq reuslt. I am wondering whether you can give me some advice. This diff result is from two cell type bulk RNA-seq. I use two specific marker to get these two cell type using Flow cytometer. I alreadly…

Continue Reading weird MAplot or volcano plot of DESeq2 diff result