Tag: glmLRT

how to test for differential expression in samples where a global increase in gene expression is expected

As the title suggestions, I’m wondering what the best way to test each gene in a count matrix containing two groups is, where one group is expected to have a global increase in gene expression. I need to use spike-in normalized RPKM data, so from my understanding of DESeq, it…

Continue Reading how to test for differential expression in samples where a global increase in gene expression is expected

A query about selecting the coefficient in glmLRT to test for by index

A query about selecting the coefficient in glmLRT to test for by index 1 @0b4d0d5b Last seen 9 hours ago Norway I am using the below set of equations for my differential expression analysis. In the glmLRT line, I was previously specifying the coef by index and since I am…

Continue Reading A query about selecting the coefficient in glmLRT to test for by index

rna seq – DE analysis tool and method for non-coding features

I am currently working with the non-coding features of A. thaliana, and trying to get the DE features. Among the three DE test methods in edgeR such as exactTest(), glmFit() and glmLRT(), glmQLFit() and glmQLFTest(), which is/are the one(s) most suitable for running DE tests on miRNA, snRNA, snoRNA, pseuogenes,…

Continue Reading rna seq – DE analysis tool and method for non-coding features

rna seq – Statistical methods suitable for DE analysis of non coding RNAs

I am currently working on DE analysis of coding as well as non-coding features of A. thaliana using the edgeR package. Is the negative binomial method that is normally used for the DE analysis of genes suitable for non-coding features such as miRNA, lncRNA, snRNA, snoRNA, pseudogenes, transposons, uORFs and…

Continue Reading rna seq – Statistical methods suitable for DE analysis of non coding RNAs

glmLRT contrast (compare group with processed/extracted group)

Hello, experts. I’m here to ask for your kind helps. I’m currently working on DEG analysis. briefly, I want to compare DEG differences between (P07_T01-P07_N01 & P08_T01-P08_N01) vs (P07_T02& P08_T02). This is to compare T01’s solely with T02’s. Yet, there are 2 problems. First, I keep getting an error from…

Continue Reading glmLRT contrast (compare group with processed/extracted group)

KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset

Hello, I am new to bioinformatic analyses and I am trying to analyse the TCGA dataset to plot a survival curve based on the expression of a gene of interest (say TP53). I have written the following code to analyse the TCGA data, but I am unable to proceed further…

Continue Reading KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset

makeContrasts design and checking for housekeeping gene expression levels?

I have 2 sets of questions about a metatranscriptomics analysis I’m working on. (1) My experimental design was to compare OG environmental samples (samples kept 30 mins at original temperature) to HT samples (environmental samples kept high temperature for 30 mins), where both OG and HT samples were in glass…

Continue Reading makeContrasts design and checking for housekeeping gene expression levels?

Differential gene expression analysis with no replicates using edgeR

Dear all, I have an experimental design where I have only one sample in each condition (2 conditions in total) and want to do differential gene expression analysis using edgeR. This is the script I want to use for the analysis and it runs without any errors – with this…

Continue Reading Differential gene expression analysis with no replicates using edgeR

Differential expression analysis of TCGA data based on tumor staging

Hi everyone I wanted to analyze TCGA-BRCA data for identifying DEGs in different TNM stages (I to IV) between Normal and Tumor. How to change the following code to get the DEGs based on the staging? CancerProject <- “TCGA-BRCA” DataDirectory <- paste0(“../GDC/”,gsub(“-“,”_”,CancerProject)) FileNameData <- paste0(DataDirectory, “_”,”HTSeq_Counts”,”.rda”) query <- GDCquery(project =…

Continue Reading Differential expression analysis of TCGA data based on tumor staging