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Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Gordon Smyth
50k
I can't tell you how to analyse your particular dataset. I can only give general advice and help with limma syntax. I don't even know what …
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, Thank you so much for your guide! I don't handle the raw data but a text file with all samples that already normalized as you s…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Gordon Smyth
50k
The MDS plot shows a massive batch effect. If this is a correct plot of your data, then any analysis you have done of this data is worthles…
Comment: Memory errors using read.bismark?
by
Peter Hickey
▴ 710
> Only one thing, my data are actually CpG methylation :) No, the file you sent me is CX methylation (i.e. CpA, CpC, CpG, CpT), as is clea…
Comment: DEG with low counts
by
Rajat
• 0
Dear Dr. Michael Thanks for you quick reply. I appreciate it. Attached is the plotcounts for one gene. I am experiencing like this in oth…
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Comment: Memory errors using read.bismark?
ashr vs apeglm for interaction data
Comment: Light difference when using coef vs omit a group when compare 3 groups.
Answer: Light difference when using coef vs omit a group when compare 3 groups.
C: Add new columns to DESeqResults from text file by matching rownames.
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