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Answer: DEseq 2 LFC shrinkage with apeglm in single-cell pseudobulk: strange volcano plo
by
ATpoint
★ 4.4k
There is nothing unusual here. There is simply no evidence for differential expression. Almost all genes are shrunken towards zero, due to …
Comment: EdgeR - Apparent Wrong Direction of logFC with Low Count Data
by
blmurphy
• 0
Hi Gordon. It was collation with my edgeR results, BASTA taxonomy, and function gene annotation tables. Prior to doing this last check for …
Answer: Poor dispersion fit in DESeq2
by
Michael Love
42k
The fit (red line) doesn't matter because you have so many samples. Note there is almost no shrinkage. Besides that you may be intereste…
Answer: DESeq2 analysis on 2 plant lines infected with virus, with 2 time points (days p
by
Michael Love
42k
I'd recommend actually meeting with a local statistician to work out the analysis plan, or someone familiar with linear models in R. I h…
Answer: DESeq2 design and contrasts with 2 drug-treated and one control group
by
Michael Love
42k
> Now I am interested in comparing the DE genes between the resistant and acute groups, but I am unsure how to account for DMSO in that com…
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A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
Comment: ISO a solution to rank-order introns by transcript
Answer: ISO a solution to rank-order introns by transcript
Answer: ISO a solution to rank-order introns by transcript
Answer: Issues with retrieving Zea mays genes dataset: biomaRt error: looks like we're c
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