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qiz218591 • 0@40dc255d
Last seen 4 weeks ago
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?
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?