Bioconductor PhenoData

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HTqPCR phenoData esetVis pData

3.3 years ago Marcelo Laia ▴ 450

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affycoretools ReadAffy Biobase phenoData affy

updated 4.2 years ago by James W. MacDonald 68k • written 4.2 years ago by bastien_chassagnol • 0

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HtqPCR grouping visualization R phenoData

5.5 years ago mohammedtoufiq91 ▴ 10

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FCS flow cytometry bioconductor phenoData Loading Data

updated 8.1 years ago by SamGG ▴ 360 • written 8.1 years ago by smajor • 0

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Comment: Use of limma R package with targeted proteomics for DE analysis by svlachavas ▴ 840

Dear Gordon, thanks a million for your reply (just saw it, did not get any notification through email) !! Regarding the log2 transformation…

Answer: cameraPR() non directional test by Gordon Smyth 52k

Yes, you can still do non-directional tests using cameraPR(), but it's not quite as easy as it was using the original camera() function as …

Answer: WGCNA with paired samples by Ivo • 0

You can use batch correction on the person ID and then continue WGCNA as usual using the corrected matrix. You can use e.g. sva::ComBat or …

Answer: Plot title for PCA in DESeq2 by ATpoint ★ 4.7k

The function uses ggplot2, so you need `+ ggtitle('title')`. Please take a ggplot2 tutorial for details.

Comment: DESeq2 It is correct to use interaction term for patient variability? by Bradley • 0

I apologize, but I am still perplexed. I need to know the exact type of replication. Do we have many samples taken from the same tumor? You…

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Answer: limma::voom vs edgeR::voomLmFit - when to use?

Comment: limma::voom vs edgeR::voomLmFit - when to use?

Answer: Plot title for PCA in DESeq2

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