Question

RPPA data (Proteomics analysis)

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qiz218591 • 0

@40dc255d

Last seen 13 months ago

India

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?

TCGAbiolinks limma • 1.3k views

ADD COMMENT • link 21 months ago qiz218591 • 0

score 0 · Answer 1 · 2023-04-01

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Gordon Smyth 52k

@gordon-smyth

Last seen 4 hours ago

WEHI, Melbourne, Australia

Manipulating results is easy in R and limma. Just read the examples and documentation, for example help("topTable").

The limma results include whatever changes are significant, regardless of fold-change sizes or directions.

ADD COMMENT • link 21 months ago Gordon Smyth 52k

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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?

ADD REPLY • link 21 months ago qiz218591 • 0