Question: Tcga Mirnaseq Differential Analysis: U-Test Or Edger-Like Approaches On Rpm Values
gravatar for B. Arman Aksoy
6.0 years ago by
B. Arman Aksoy1.2k
New York, NY
B. Arman Aksoy1.2k wrote:

Let's assume that I have two conditions and I would like to do a differential miRNA expression analysis between these two groups. I have log2 "reads per million" (RPM) values as my input data set. Now, I am wondering whether I should test the differential expression between these groups using a Mann-Whitney-U test on log2 RPM values or feed these reads to a edgeR/limma.voom/DESeq and run the regular RNASeq differential gene expression pipeline on them as if they are RSEM values?

ADD COMMENTlink modified 6.0 years ago by Devon Ryan94k • written 6.0 years ago by B. Arman Aksoy1.2k
gravatar for Devon Ryan
6.0 years ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:

I would suggest the limma/voom route unless you don't plan on sharing information across genes. I should also note that you should read through this thread on the Bioconductor email list regarding TCGA data and limma/edgeR/etc. There's also mention in that thread of the fact that the "normal" controls in TCGA are often far from being an appropriate comparison group.

ADD COMMENTlink written 6.0 years ago by Devon Ryan94k
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