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Dear all, I have a doubt-
I performed, the limma on the RPPA data file from TCGA- therefore generally if I would ask- Is it possible to have the high negative logFc value (downregulated proteins) as compared to low positive logfc(upregulated proteins) in the results after the differential expression analysis through limma in r?
Thank you
I just have another question, can we use the limma or edgeR package to do the subtype specific differntial expression analysis ? If not then what are the barriers which made it to not do it? and what other package or concept can be applied to do this analysis ? I found one package called http://bioconductor.org/packages/release/bioc/html/OVESEG.html but I am not confident about it, as there are very less publications on it. Also it is more delineated towards immune cells. How about taking the subtype from the TCGA-BRCA and do the DE anlayais with edgeR and limma ? would that conceptually and scientifically fits?