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Comment: Help with model.matrix and creating the right contrast matrix for limma
by
Gordon Smyth
48k
> Does this mean there is an anova test comparing the mean expression of each gene for each contrast specified (LvsC_m5 and HvsC_m5)? So wh…
Comment: TPM to raw counts
by
bella.johnson.2022
•
0
I know this is a bit of an old thread, but I used `'tximport'` to take my TPM output from Salmon and get the raw counts to then run DESeq2 …
Comment: Ensembl down???
by
James W. MacDonald
64k
Yes, you have already said that. The length of the lists isn't material to this discussion, but the nature of the IDs is. I have no idea wh…
Comment: Ensembl down???
by
bas_work
▴
20
Thanks, I'm now exploring these. I want to map external gene names (long lists, actually) to human HGNC symbols and Ensembl gene IDs...
Comment: Different results from blockwiseModules and blockwiseConsensusModules individual
by
James W. MacDonald
64k
Why do you think the modules for an individual block should be remotely similar to the consensus modules generated using all the blocks? Di…
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