Bioconductor Affyexpress

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folder quality QualityControl AffyExpress

4.1 years ago bastien_chassagnol • 0

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AffyExpress AffyExpress

updated 12.5 years ago by Sean Davis 21k • written 12.5 years ago by Guest User ★ 13k

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cdf simpleaffy AffyExpress cdf simpleaffy AffyExpress

17.3 years ago Stefan Thomsen ▴ 50

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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…

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

All you have done is set up a `DESeqDataSet` object and then run `vst` on it. That won't affect the PCA plot at all - you are simply tellin…

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A: Trajectory analysis for single cell sequencing

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