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Bioconductor ALL

18 months ago • updated 17 months ago simone.tiberi • 0

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ALL The DifferentialRegulation PathNet

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updated 2.3 years ago by James W. MacDonald 67k • written 2.3 years ago by xxxsarahkimxxx • 0

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biocLite update all default ask

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bioconductor ALL linear model

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ALL bioconductor biobase exprs

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installation packages bioconductor all

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Answer: ANOVA like approach of edgeR by Yunshun Chen ▴ 870

You could try the followings: > design <- model.matrix(~ 0 + group) > contrast <- makeContrasts(PvsL = 0.5*(L.pregnant + B.pregnan…

Answer: Identical samples after deseq2 batch effect removal by maripane • 0

Thanks Michael, so is there a way to work around this issue? Can I somehow make sure I can remove this batch effects without overcorrecti…

Comment: CleanUpRNAseq with a GTF that is missing mitochondria annotation data by rcreed • 0

The updated version worked well on my data. Thank you!

Answer: DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 di by James W. MacDonald 67k

The two contrasts at the bottom are identical but for the sign of the logFC, so you should expect the same results (except for flipped sign…

Comment: Identical samples after deseq2 batch effect removal by Michael Love 42k

Oh, i didn't realize there is another method in the mix here. I would not necessarily trust this "batch correction" method, and suspect o…

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Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data

A: TopGO: How to retrieve the gene list related to a GO ID ?

A: Error in DESeqDataSet : some values in assay are not integers

A: correcting the batch effects in Limma and SVA

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Scholar to Haibo Liu ▴ 20