Tag: dgelist

TPM normalization starting with read counts

Hello everyone I have multiple bulk RNA-seq datasets that I need to apply the same pipe line on. I want to normalize them from counts data to TPM. In all datasets, I have the genes as rows, and samples as columns. Unfortunately, I don’t have the fastq files, all I…

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I have a query regarding differential gene expression using limma-voom.

I have a query regarding differential gene expression using limma-voom. 1 @28946033 Last seen 1 day ago India I used the following pipeline for RNA Seq Analysis Fastq-Trimmomatic- Hisat2(gtf file was annotated)-featurecounts After featurecounts I tried to do limmavoom, but I get error saying this An error occurred with this…

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Gene Expression Analysis Steps ?

Hi everybody, I’m new in this field. I’m trying to replicate a paper to train my self . The results come out pretty the same but not exactly the same, so I wanted to know if all my steps are right or if I’m missing something ( or even completely…

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rna seq – R – [DESeq2] – How use TMM normalized counts (from EdgeR) in inputs for DESeq2?

I have several RNAseq samples, from different experimental conditions. After sequencing, and alignment to reference genome, I merged the raw counts to get a dataframe that looks like this: > df_merge T0 DJ21 DJ24 DJ29 DJ32 Rec2 Rec6 Rec9 G10 421 200 350 288 284 198 314 165 G1000 17208…

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Unsuccessful DE analysis using limma

This might be a bit long, please bare with me. I’m conducting a differential expression analysis using limma – voom. My comparison is regarding response vs non-response to a cancer drug. However, I’m not getting any DE genes, absolute zeros. Someone here once recommended not to use contrast matrix for…

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Removing replicate not clustering and group with replicate Vs without -edgeR rnaseq analysis

Removing replicate not clustering and group with replicate Vs without -edgeR rnaseq analysis 0 I am working with bacteria samples – in 3 groups that include the control, Treatment A, and Treatment B. From the PCA I find that the replicates are far apart. So I have removed the treatment…

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r – Contrast for Limma – Voom

I’m doing a differential expression analysis for RNA-seq data with limma – voom. My data is about a cancer drug, 49 samples in total, some of them are responders some of them are not. I need some help building the contrast. I’m dealing with only one factor here, so two…

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Limma Differential Analysis on Proteomics data

Limma Differential Analysis on Proteomics data 1 @3c9b3fdc Last seen 7 hours ago United States Hi, I have a proteomics data set and I am doing the differential analysis on that. I used the Limma package to do that. I first removed the negative counts and did the analysis but…

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DGE from tumor-adjacent normal pair RNA-seq data. For an individual, no replicate

Single sample analysis can be done in edgeR, while it is deprecated in DNASeq2 in 2018 probably (if you can use old DESeq version then it will work in single sample also). For egdeR you just do library(edgeR) setwd() rawdata <- read.delim(“filename”, check.names=FALSE, stringsAsFactors=FALSE) ngenes <- 10000 #no. of genes…

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keep only genes expressed in sample at the same time as a particular gene of interest

Filter DGElist object: keep only genes expressed in sample at the same time as a particular gene of interest 0 Hello, need some help here as I’m kind of stuck with the edgeR DGElist format. I have a DGE list named x with the following dimensions: > dim(x ) [1]…

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Calculate fold change in edgeR with one sample per condition

Hi, We have run a pilot RNA-Seq study with one sample per condition, this is just a test run. I understand there is no valid statistical test in this case, however just curious to obtain differential expression through edgeR package in R assuming dispersion = 0.4 for the human data….

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