Tag: log2FoldChange

DESeq2 for different design and normalized counts 0 Hi, I have normalized count data from RNA-seq protocol. The normalization steps include DESeq2 with design ~1. Unfortunately, I do not have the raw counts. Can I use those normalized counts for DESeq2 with different design? Thank you. DESeq2 log2foldchange • 84…

Hi all, I successfully ran DESeq2, though I am looking for differential abundance of microbial genera, not gene expression. However, duplicate genera (assigned to different species in my taxa table) are listed out and numbered instead of collapsing. I would like to collapse duplicate genera. Here is what I ran…

Hi all, I am working with the RNA-Seq data on human (24Cases-20 controls) to find differentially expressed genes. my RNA-Seq data is unstranded. Here is the comments that I used to align the fastq files: ls *_1P.fastq.gz | parallel –bar -j8 ‘R2=$(echo {} | sed s/_1/_2/) && out=$(echo {} |…

In geom_tile the size aesthetic only controls the size of the line (now replaced by linewidth in newer versions of ggplot2). The tiles themselves cannot really change size as their filling of the whole space is part of how that geom represents data. You can use geom_shape with the squares…

DESeq2 with multiple factors 0 I have 18 samples. These samples have 2 different factors with one factor(Infestation) having 2 levels (as control vs affected) & another factor(timepoint) having 3 levels(as 24h, 48h,96h) . Also the last factor (timepoint) have 3 biological replicates. While performing: counts <- read.delim(“counts.csv”, header =…

Hello! I’m needing some help from the more experienced ones! n_n’ I’m doing a transcriptome expression comparison using DESeq2 and I would like to be sure I’m using the right parameters. This doubt came after seeing that a gene increased the expression between different sampling points but was not included…

My Volcano plot is working fine for the argument on one shape for all as below; EnhancedVolcano(res_df, lab = res_df$gene_sym, x = ‘log2FoldChange’, y = ‘pvalue’, title=”MSC Cellular RNA vs MSC Exosome”, pCutoff = 0.05, FCcutoff = 1, pointSize = 3.0, labSize = 6.0, shape = 23, colAlpha = 1)…

data file link: drive.google.com/file/d/1Odr12yDiUwI02-BfaXrHehKBM1uMW_1N/view?usp=share_link Step 1 (5pts) Load the file GSE124548.raw.txt into R and create a new dataframe with just the columns with the raw counts for healthy (HC) and CF patients before treatment (Base) and call it readcount. Use the first column (EntrezID) in the original file as the…

Hi guys, I’m relatively new to any type of analytics work and Rstudio. However, when inputting my TCGA data and doing all of the basic steps, my volcano plot and log2foldchange values seem to all be the opposite of what was expected. I understand perhaps this could just be the…

Background: Choledochal cysts (CC) are congenital bile duct anomalies with 6-30% risk for developing bile duct cancer. However, the molecular mechanisms underlying cancer risk of CC are unknown. We sought to identify the gene expression changes underlying the cancer risk of CC patients. Methods: Liver organoids (n = 51) were…

Meaning of stat values in DESeq2 result 1 Hello, experts. I’m curious what will be the meaning of stat values in the DESeq2 result. For example, if geneA has a stat value for 50, and geneB has a stat value for 20, what is the overall comparison meaning of these…

Hi! Apologies for the stupid question! but I think I am doing something wrong but i do not understand what. I would like to do ORA analysis on bulk-RNAseq dataset so I tried both clusterProfiler and also genekitr.` However, despite getting the same terms, but I have different p-adjusted value…

I am working DESeq2 i wanted i proper boxplot but i don’t understand what wrong i am doing and i wanted to know how to properly plot the x and y axis what parameters should be taken for boxplot . here’s my code: library(“DESeq2”) library(“ggplot2”) counts<-read.delim(“PC_1.csv”,header = TRUE, row.names =…

Extract/include transcript list from GAGE analysis result 0 Hi everyone, I’m using GAGE following Deseq2 analysis on my RNAseq data. This means, the analysis is being done on log2FC. I can’t see any list of transcripts related to GO terms/pathways that are being enriched. Something like the usual tools of…

DESeq2 for time series and control-treated groups 0 Hi, I am new at DESeq2 and trying to desing matrix to get DEGs. Basically, I need number of DEGs based on compare control/treated groups each time points. I tried dds <- DESeqDataSetFromMatrix(countData = round(counts_data), colData = colData, design = ~time +…

Hi, I am using DeSeq2 to estimate the DEGs across a dataset of 6 samples with 3 samples each in 2 conditions – patient versus control. The parameters for the DEGs are as follows: |Log2FC|<2, P-value<0.05 I ran DeSeq on the datasets through 2 ways – (i) Without the LFC…

Hi everyone, I would like to colour a specific population of genes in a volcano plot using enhanced volcano function. The thing is they are crowded in the rest of the non-significant genes. Would like to overlay them to be visible. Here is the code used keyvals.colour <- ifelse( res_table_tb_sex$ygenes…

gseKEGG – no gene can be mapped (RNAseq analysis) 0 Hi all, I have been trying to extract the GSEA results from a list of genes after RNAseq analysis. It looks like my gseKEGG function is giving me problems. I am unable to generate a list of KEGG terms, it…

Identifying differentially expressed genes (DEGs) is an important task in genetic research because it allows researchers to identify genes that are associated with a particular phenotype or condition of interest.DEGs are genes that show significant differences in expression levels between two or more groups, such as a disease group and…

Hello everyone, I have a list of differential genes (list1) and another list where I have the ID of the genes and the name (list2) and I want to name the genes from list1 taking the name from list2, how can I do this? I will appreciate your support, thanks….

Hello community, I’m relatively new to DGE/DEG analysis using RNA-Seq data, for which I’ve seen that DESeq2 is one of the go-tos for differential gene analysis. I am a bit confused about the list of genes I am obtaining and which type of normalization methods are best to use (variance…

I am performing a differential expression analysis for collaborators. The overall biological design from my collaborators is as follows: 1) Received patient sample. 2) Amplified patient sample using patient derived xenograft (PDX) in a mouse host. 3) Extracted cells from mouse and enriched for human cells by positive selection using…

Hi, I’m sure I’m missing something obvious, but is there an easy way to access the gene symbols after adding them with the addIds() function in tximeta? gse <- addIds(gse, “SYMBOL”, gene=TRUE) mcols(gse) DataFrame with 60240 rows and 3 columns gene_id <character> ENSG00000000003.15 ENSG00000000003.15 ENSG00000000005.6 ENSG00000000005.6 ENSG00000000419.12 ENSG00000000419.12 ENSG00000000457.14 ENSG00000000457.14…

Help for RNA sequencing analysis with DESEQ2 0 @80066fff Last seen 1 day ago Canada Hello everyone, I’m currently trying to perform DESEQ2 with my own RNA sequencing results. I performed whole transcriptome RNA sequencing and the subsequent analysis I performed via galaxy. I performed first fastp on the samples,…

Introduction Multiple myeloma is a B-cell malignancy characterized by the malignant proliferation of clonal plasma cells in bone marrow,1 It is the second most common hematological malignancy after lymphoma.2 The age-standardised rate (ASR) of multiple myeloma incidence was 1·78 (95% UI 1·69-1·87) per 100 000 people globally and mortality was…

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…

Correlation between two different datasets: between results of RNAseq and absence/presence of Type3 Secretion System 1 Dear All, I have a “How would you solve” kind of question. I have two sets of tables : 1. Log2FoldChange table and 2. Effectors Table. Firstly, the Log2FoldChange table was obtained by performing…

Dear Experts, I have RNAseq data from 6 different plant samples (2 control, 2 Sensitive, and 2 tolerance), and different location of one species. I am trying to see the effect of the different groups at different time points, but after going through all the posts and vignettes I am…

InteractiveComplexHeatmap on DESeq2 object with more than 2 groups 1 Hello all, I’m writing with the hope someone can clarify a doubt I have about the differential heatmap generated by the package InteractiveComplexHeatmap via the simple command interactivate(dds). I read the package documentation at bioconductor.org/packages/release/bioc/html/InteractiveComplexHeatmap.html, but I couldn’t find the…

Genes looking differential abundant are not accoring to DESeq2 0 I have a metagenomic dataset crossing three time points from which I have mined CAZymes and am using DESeq2 to identify differentially abundant CAZymes from using trimmed mean depth generated my CoverM (very similar to Q2Q3 contig coverage). From this…

I have a result from which I want to get significant genes (pvalue-threshold=0.1, log2FoldChange threshold 1.5), and divide them into up-regulated and down-regulated. From the vignette, I found the following on down-regulation and up-regulation: subset the results table to these genes and then sort it by the log2 fold change…

I’m trying to set a threshold with different criteria to label data points into categories So my code is this C1_C2 = read.csv(“C1_C2_contrast.txt”) diff_C1_C2 <- C1_C2 %>% mutate(UP_DOWN = case_when( # padj < 0.05 & log2FoldChange > 1.5 & log2FoldChange < 2.5~ “UP”, baseMean > 50 & pvalue < 0.05…

Introduction Rotator cuff tear (RCT) is a common shoulder disorder causing shoulder pain and disability. The prevalence of full-thickness RCT is 20.7% in the general population, and increased with age.1 Rotator cuff play essential roles in shoulder function and the treatment of proximal humeral fractures.2,3 It is important to repair…

How to do functional analysis on differentially expressed gene list from RNA-seq data? 0 @06f08eeb Last seen 1 day ago Canada Hi all, I am a complete beginner in terms of bioinformatics analysis and I am hoping to complete some functional analysis on some differentially expressed gene lists of some…

My data is experimental data that has been overexpressed for a specific gene. Data samples are divided into 3 groups according to the over-expression time and each group has 3 samples. (total 9 samples) I conducted DGE analysis on the control group and one case group with DESeq2. cts <-…

You can use base R graphics to make these plots. The data is sitting there in columns of the res object, so you can filter it directly, and use boolean vectors to pick out the things you need: # make sure there are no NA values sum(is.na(res$log2FoldChange)) # choose some…

sigh of log2FC values in DESeq2 0 @194b0276 Last seen 10 hours ago United States Can someone explain to me how is the sign of log2FoldChange is set in the results of DEseq2? I was pretty sure that it is calculated as log2(Counts_treatment/Count_reference), where reference is determined alphabetically (unless specified…

highlighting specific genes (from a user-supplied list) in a Volcano plot in R 1 I’ve generated a volcano plot using DeSeq2 results and would like to specifically highlight a subset of genes by providing a list of gene IDs Dataset$condition <- relevel(Dataset$condition, “Ctrl”) res <- lfcShrink(DatasetProcessed, contrast=c(“condition”,”Treat”,”Ctrl”)) with(res, plot(log2FoldChange, -log10(pvalue),…

TPM value from DESE2 and significant filterig isssue 0 The code 10101 res_ddsDE_new has 36,000 rows. When I am using subset(res_ddsDE_new, padj < 0.05 & abs(log2FoldChange) > 1) res_ddsDE_new baseMean log2FoldChange <numeric> <numeric> DDX11L1 1.779144 -1.4955939 WASH7P 152.518293 -0.0505911 MIR6859-1 20.653876 0.5689275 MIR1302-2HG 0.255387 -1.9691031 FAM138A 0.353478 0.1574042 Then I…

Are zero is a default option of log2fold change to be considered as up and down? Yes, by default, the null hypothesis is that the log2FoldChange is zero. Does this mean that there are seven genes in total that will have significant adjusted p-value? Yes, you are interpreting your results…

DESeq2 log2FC and p-value filtering 1 Dear all, I want to filter DE genes by log2FC > 2/-2 and p-value 0.0001. Why this two versions of lof2FC and p-value filtering differ in up- and down-regulated genes numbers (from 800 to 1500) and which one is the right one ? 1….

I have a project where I have done RNA-seq (paired-end sequencing on Illumina HiSeq) of a worm at different days of development i.e. Ages 0-12. For each age, I have sequenced 3 replicate specimens. I’m new to DESeq2 and I was wondering if what I did below is correct. library(DESeq2)…

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…

Need help to remove NA values from data frame 2 I have this data frame : and I want to remove those rows which contain NA values from the log2fold change column How can I do this through R? DeSEQ2 R • 256 views Hi Anas, If your data frame…

I am making a volcano plot for my phosphoproteomics data and seemingly the data are not centered around the origin. The reason that I know there is something wrong is because before my code was producing the correct volcano plot, and now it is shifted. What are some reasons why…

Hi guys, I’m working with a 8 samples experiment (lower than 3x replicates, I know..) with a design like > colData(dds) DataFrame with 8 rows and 2 columns condition traitment <factor> <factor> 4200-JS-1 norm ctrl 4200-JS-2 norm ctrl 4200-JS-3 norm trt 4200-JS-4 norm trt 4200-JS-5 hyper ctrl 4200-JS-6 hyper ctrl…

Is it a good idea to plot a volcano plot starting at position x =1 1 Hello everyone! I was wandering if it makes sense to start a volcano plot (x=log2FoldChange) starting at position one, so basically discarding all values below 1 and above -1 leaving only values outside this…

I am new to circos plot analysis and have been trying to use the cyclize package. I want to display mRNA differential gene expression data based on data analyses of 8 libraries and links between their respective target genes. The dataset I am working with looks like this geneid baseMean…

Hi, Dr love. I post a question about weird MAplot or volcano plot of DESeq2 diff result and also in biostar. ATpoint give a useful answer about too many 0 count genes and prefiltering. It seems that too many 0 count genes makes lfc shrink have a probelm. And I…

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…

Hi everyone, I have done a pair comparison with DEseq2 to find differentially expressed genes between two samples with 6 replicates, for the DEseq2 result, i got exactly same padj value for all the genes and it is not significant, is this normal ? I don’t think the padj should…