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Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
Tim Peters
▴ 200
Also, re DMR.plot(), yes the understanding is that all DMRs from EPICv2 should be plotted in hg38. I've left that implied for the user sinc…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
Tim Peters
▴ 200
Hi Xiaofei, Thanks for this. If your data is from 450K, you'll have to call your DMRs in hg19, and then lift the DMR ranges over to hg38 p…
Comment: Deseq2 Design
by
James W. MacDonald
67k
You could do that, but if we assume the within-group variability is similar across groups, you gain power by fitting a single model and ext…
Comment: Deseq2 Design
by
pm_25
• 0
Thanks James, I went ahead and fit the model for cell means as so: ```r dds <- DESeqDataSetFromTximport(txi, colData = sampleTable,~Condit…
Answer: Build error on kunpeng2 Linux aarch64
by
James W. MacDonald
67k
This isn't the place for developer questions. Please use the developer listserv at bioc-devel@r-project.org instead. Also, you might wan…
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DiffBind giving different results from dba.report() and dba.analyze(..., bRetrieveAnalysis=TRUE)
Answer: Deseq2 Design
Answer: Fold change calculation in Diffbind vs. DESEQ2?
Fold change calculation in Diffbind vs. DESEQ2?
FeatureCounts Output Counts at Exon Level Using Default Settings, want gene level
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