User: derricca0708

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derricca070810
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Posts by derricca0708

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Comment: C: GSVA analysis and limma feature
... Thank you again for the answer.. I'm not familiar with the limma pipeline, but I found **makeContrasts()** and other codes in Limma users guideline's 9.3 Several Groups. It explains how to compare three groups. > adjPvalueCutoff <- 0.05 > > logFCcutoff <- log2(2) ...
written 5 months ago by derricca070810 • updated 5 months ago by Kevin Blighe28k
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Comment: C: GSVA analysis and limma feature
... Thank you for the quick and kind answer... By 'repeat code 3 times', do you mean that I'll have to repeat the code > sig.genes <- c(names(res[res[,2]==1,2]), names(res[res[,2]==-1,2])) > lung_eset.siggenes <- lung_es[which(rownames(lung_es) %in% sig.genes),] to > sig.genes1 < ...
written 6 months ago by derricca070810
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GSVA analysis and limma feature
... Hello, I'm working on GSVA and further analysis using Limma just like the https://bioconductor.org/packages/release/bioc/vignettes/GSVA/inst/doc/GSVA.pdf figure 4. My data is clustered into 3 types, according to the TCGA protocol for LUAD. I followed the description from the GSVA.pdf and the answ ...
gene R written 6 months ago by derricca070810 • updated 9 days ago by RamRS17k

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