I am very new at RStudio and differential expression analysis and I am a bit lost about what to do.
I received 2 tables of gene expression on dataframe One with the studied cells, other with control group. The data doesn't come on rawcounts, but in quantile normalized data (with RMA). I tried but couldn't create a DESeq2 object and looks like I can only use rawcounts for it. I can't have access to the rawcounts and those 2 tables were all I got.
The authors say:
The .CEL files of control group were downloaded and data were normalized using the GeneSpring GX software (version 11, Agilent Technologies) and the Robust Multi-array Average (RMA) algorithm for summarization (which uses Perfect Match (PM)-only based measures) and quantile normalization, and then exported.
The "value" output == RMA normalized intensity values (no baseline transformation). I have, however, a *.csv file.
What should I first do with it? Could you help me with which steps and which package I can use? Now I've been checking limma, but I am having problems to find out how I can create the object for the package.
Best regards, Mari