Tag: glmLRT
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…
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…
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…
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 =…
