Tag: modelr

Dear all, I am doing a DGEA with DESeq2 and data imported with tximport. I have an unbalanced dataset as reported below. With the counts and the metadata that I have I would like to answer different questions. I would like to look at the differential expressed genes between the…

Dear all, I am doing a DGEA with DESeq2 and data imported with tximport. I have an unbalanced dataset as reported below. With the counts and the metadata that I have I would like to answer different questions. I would like to look at the differential expressed genes between the…

With help from this forum, I was able to get R and RStudio working on Zorin 16 Lite. I now need to install the ‘tidyverse’ package for R, but attempting the install gives this error: $ sudo R (R starts up) > install.packages(“tidyverse”) Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is…

Introduction Questions Variation Visualizing Distributions diamonds %>% ggplot(aes(x = cut)) + geom_bar() diamonds %>% ggplot(mapping = aes(x = carat)) + geom_histogram(binwidth = 0.5) diamonds %>% filter(carat < 3) %>% ggplot(aes(x = carat)) + geom_histogram(binwidth = 0.5) diamonds %>% ggplot(aes(x = carat, color = cut)) + geom_freqpoly() ## `stat_bin()` using `bins…

`MOFAobject@expectations` is empty list 0 Hello I run the tutorial (raw.githack.com/bioFAM/MOFA2_tutorials/master/R_tutorials/CLL.html) library(MOFA2) library(MOFAdata) library(data.table) library(ggplot2) library(tidyverse) utils::data(“CLL_data”) MOFAobject <- create_mofa(CLL_data) MOFAobject data_opts <- get_default_data_options(MOFAobject) model_opts <- get_default_model_options(MOFAobject) model_opts$num_factors <- 15 train_opts <- get_default_training_options(MOFAobject) train_opts$convergence_mode <- “slow” train_opts$seed <- 42 MOFAobject <- prepare_mofa(MOFAobject, data_options = data_opts, model_options = model_opts, training_options =…

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 =…

How to extract proteins from PCs in plot_pca in DEP package? 1 I am using DEP package to analyze proteomics data. I did PCA for my samples (see the following plot) and wish to extract proteins in PC1 for further analysis. However, the objects x and y generated by the…

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…

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 =…

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…

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…

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…

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…

I am attempting to plot the below vector, but when I run the function, it just continues to run and does not plot. I have waited 5 minutes before I feel uncomfortable and click stop in the console. Wondering what is going on. Up until this point I have had…

TLDR: Example R function to calculate significance of overlap of 2 or more gene sets. genes_all is a vector that contains all genes, and gene_sets takes a list of vectors for each gene set. I encourage people to read the full tutorial and attempt to reproduce the code themselves (especially…