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mani2012 / BatchQC

Provides Quality Control of sequencing samples by deducing if there is batch effect and adjusts for it.
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data is always log2cpm transformed in correlation.R #13

Open nrachman opened 5 years ago

nrachman commented 5 years ago

from looking at the source code, I am under the impression that data is always transformed to log2cpm when performing the correlation analyses in correlation.R even when log2cpm_transform = FALSE

I was using batchQC on microarray data and my data are already log transformed. Though subtle, the additional log transformation does affect the median pairwise correlations

using batchqc_corscatter - matches output from from batchQC(..., log2transfrom = FALSE) image

modified batchqc_corscatter to not log2 CPM transform image