Bioconductor GCMAP

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microarray cmap package gCMAP gCAMPWeb

updated 5.1 years ago by Martin Morgan 25k • written 5.1 years ago by bastien.chassagnol • 0

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rnaseq drugvsdisease gcmap gcmapweb

updated 7.7 years ago by saezrodriguez • 0 • written 7.7 years ago by bioinformatics ▴ 20

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gCMAP gCMAPWeb

9.7 years ago • updated 9.6 years ago afshinmh • 0

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gCMAP gCMAP

updated 11.6 years ago by Dan Tenenbaum ★ 8.2k • written 11.6 years ago by Christopher Howerton ▴ 40

4 results • Page 1 of 1

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Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D by James W. MacDonald 67k

How you analyze your data is up to you. But do note that Subset * Conditions implies that you want to find genes that respond to stimulus d…

Comment: MBDseq analysis using qsea package by kf • 0

Hi Matthias, Happy new year! I wondered if it is possible to retrieve normalized value from each samples? makeTable seems only return beta…

Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D by Quang • 0

Hi, James. I forgot to mention, but yes, I did run `DESeq2::DESeq()`. So, I ran `DESeq2::DESeqDataSetFromHTSeqCount`, then `DESeq2::DESeq()…

Answer: Why did PCA plots look exactly the same after adjusting for batch covariate in D by ATpoint ★ 4.6k

It's an FAQ in the vignette: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#why-after-vst-are-there-s…

Comment: Deseq2, enrichGO and ensembl ID by James W. MacDonald 67k

I am not sure I understand. You say that a unique Ensembl ID maps to multiple gene symbols. That doesn't mean you have two genes (it's just…

Votes

A: Trajectory analysis for single cell sequencing

Answer: Annotation with org.Hs.eg.db Genome Build 38

Answer: Considerations behind the choice of RNAseq Differential Expression Analysis Tool

A: goana limma- extract list of DE genes and genes in the enriched GO terms?

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