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User: grimmerucsf

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Posts by grimmerucsf

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Comment: C: DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
... If the batch designations come into play later in the DE calculations, but not at all in the transformations, it seems that ComBat may be the culprit. Thanks! ...
written 5 months ago by grimmerucsf • 0
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DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
... We have three RNA-seq batches for ~60 samples where batches are known and the "condition" is not well-distributed across batches. For example: batch A = all tumor subtype 1 batch B = all tumor subtype 2 batch C = a mix of subtype 1 and subtype 2   For this reason, I suspect batch correction may ...
sva deseq2 combat rna-seq written 5 months ago by grimmerucsf • 0 • updated 5 months ago by Michael Love ♦ 21k
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Answer: A: package 'ChAMP' demo/test code fails at champ.CNA()
... Changing all "C" values in the "Sample_Group" column to "Control"  in the csv file worked for me. ...
written 3.0 years ago by grimmerucsf • 0

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