Bioconductor RTANDEM

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peptide peptideidentification rTANDEM MSGFplus Alternatives

updated 8 months ago by shepherl 3.5k • written 8 months ago by vaddanki ▴ 10

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Comment: Exporting DESeq2 filtered results by camillab. ▴ 10

can you elaborate? I am confused. I have the same problem: cond1 <- results(dds, contrast=c("condition","Patient","Control"), alpha = …

Comment: Effect of lfcThreshold on p-value in DESeq2 by camillab. ▴ 10

great so the best approach would be using the lfcThreshold parameter to make sure that both p.value and log2fc are taken into account in t…

Comment: HTSeqGenie runs very slow by zh9118 • 0

I found that it's always the last chunk that took time forever, even though the last chunk is the smallest one. ![enter image description …

Answer: Error MakeOrgPackagefromNCBI by James W. MacDonald 63k

You will rarely find a particular strain in any annotation data, and instead you should use the 'main' taxon ID, which for *A. baumannii* h…

Comment: Setting up a multi-factor experiement by john.briseno • 0

thanks, will do! we work with a non-model organism, but perhaps the folks who do our genomics/sequencing have some input.

Votes

A: Effect of lfcThreshold on p-value in DESeq2

Comment: Mixed up sample info with plotPCA

Answer: Setting up a multi-factor experiement

Answer: Mouse to Human Genes using bioconductor

Mouse to Human Genes using bioconductor

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