Hello everyone. I have obtained nCounter data on tumor samples of 4 distinct subgroups of one tumor type. I want to perform differential expression analysis between these 4 subgroups and get a heatmap that can differentiate between them.
My search tells me that because nCounter data are read counts (like in RNA-seq) I could use the DESeq2 package in R to do it. However, some of them also refer different types of normalization methods for the data. I am very new to bioinformatics analysis and have a hard time understanding these nuances. I have both the raw data and also the normalized data that was normalized in nSolver using their pre-defined method.
What shoul I be doing to perform the differential expression analysis? Use the raw counts data directly into DESeq2? Use the normalized data? Use a different package than DESeq2? Is it possible to perform this analysis between 4 different groups?
Hope you can help me and thank you in advance!
Ok, thank you!