Question: sva/ComBat with missing values?
3.6 years ago by
wrighth • 260
wrighth • 260 wrote:
Hi, all; I have a 224-gene OpenArray RT-PCR data set that I'm analyzing, and I strongly suspect one of the runs is having a batch effect on the entire experiment from EDA and analysis of the quality values. Unfortunately, this means that there are a number of missing values in the matrix (though not all from the suspect run). If I pull the genes containing these values, SVA/ComBat works nicely to clean up the data that remains; if I don't, it fails with a "system is exactly singular" Lapack routine error. Is there any way to force these functions to use something like the "pairwise.complete.obs" from cor to work around the missing values, or is my only option to drop genes? Hollis Wright, PhD Ojeda Lab, Division of Neuroscience Oregon Health and Science University
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