Bioconductor PCATools

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DESeq2 eigencorplot PCAtools

updated 3 hours ago by Michael Love 42k • written 21 hours ago by BioinfGuru ▴ 30

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DESeq2 PCAtools

updated 18 days ago by Michael Love 42k • written 19 days ago by Aaliya • 0

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DESeq2 RSTUDIO PCAtools

updated 19 days ago by swbarnes2 ★ 1.4k • written 21 days ago by Aaliya • 0

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Answer: Assymetric MA plot with no overall trend by Michael Love 42k

> so many upregulated genes vs. downregulated, which I think is worrying Take a look at the plotCounts for a couple of the up-regulated …

Comment: Can I trust the differential expression analysis when the two groups overlap on by Michael Love 42k

I'm wondering about sample table mixup. How have you merged your sequencing data with the phenotype data (`colData`)?

Comment: Can I trust the differential expression analysis when the two groups overlap on by Eric Katagirya • 0

Thanks @mikelove , Using vst or rlog doesn't improve the segregation nor is there a remarkable difference when I use 1000 or 2000 most vari…

Answer: Batch effect correction: methylome data by zhouwanding ▴ 10

I agree that the batch variable should be better modeled as a co-variate than explicit batch correction. There is also RUVm (https://www.nc…

Comment: Can I trust the differential expression analysis when the two groups overlap on by Eric Katagirya • 0

Thanks @bioinfguru - I did the 3-D PCA plot ![PC1 vs PC3 plot][1] and also the scree plot ![Scree plot][2] but couldn't make much of the…

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Ensembl 112 has been released.

A: Diffbind results - non uniform width

Answer: Error EPICv2 ChAMP

Comment: Store output of matchPWM()

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