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Comment: Can I trust the differential expression analysis when the two groups overlap on
by
BioinfGuru
▴ 30
No worries, wish I could be more help. Plotly provide a [3-D plot][1] function that's pretty simple (the two you did are still 2-D plots, t…
Comment: Can I trust the differential expression analysis when the two groups overlap on
by
Michael Love
42k
If you manually compute PCA on VST data, what are the top 5 genes contributing to PC1? https://github.com/thelovelab/DESeq2/blob/devel/R/p…
Comment: Can I trust the differential expression analysis when the two groups overlap on
by
Eric Katagirya
• 0
I created a DESeqDataSet object using DESeqDataSetFromMatrix function. I don't anticipate any mismatching or mixup of sampleIDs.
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`)?
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Answer: Can log2cpm be used for proteomics data normalization?
Ensembl 112 has been released.
A: Diffbind results - non uniform width
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Answer: Error EPICv2 ChAMP
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