In this thread, I will be posting about my experiences implementing DGEA packages for the data I am working with, and the types of questions we are interested in asking.
This past week I spent time understanding a little about the various packages that are out there. It is very important to understand the nature of your input data (RNASeq vs microarray, which technology platform was used eg Illumina, Affy, etc. and whether or not and how the data was normalized).
I am working with level 3 RNASeqv2RSEM data from TCGA. Upon scourging the various confusing forums and literature out there, I decided to go with the EdgeR package in R for DGEA (see attached slides ).
I modified and ran script in RStudio and I was able to get the DGEA lists (log2FC, logCPM, p-values) for the two groups I was comparing. I then used Excel/OfficeLibre to generate a volcano plot of the data. Next week I will post more about the actual script I used.