Bioconductor TempO-seq

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limma dose-response lincs tempO-seq high-throughput transcriptomics

updated 7.2 years ago by Gordon Smyth 52k • written 7.2 years ago by Pekka Kohonen ▴ 190

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Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by anna.cot.anna.cot ▴ 30

Thank you! This is actually quite close to my real dataset. I simplified the names to make it easier as an example, but I have now correcte…

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Tim Peters ▴ 200

Hi Xiaofei, Is it possible to generate a matrix of beta values or M-values with rownames as probe IDs from this data? If so, cpg.annotate(…

Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k

That looks basically correct, although the terms that you are inputing to `makeContrasts` do not match the condition names in the targets f…

Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by James W. MacDonald 67k

Oh, right. There's two ways to enter code. If you are in the middle of a sentence and you want to include a function name, you wrap the nam…

Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by anna.cot.anna.cot ▴ 30

Thank you James, that really helped! I tried CODE `enter code here` but I must have dome it incorrectly, as it showed all in red.

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