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Question: sva/ComBat with missing values?
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gravatar for wrighth
4.1 years ago by
wrighth260
wrighth260 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
ADD COMMENTlink modified 4.1 years ago by Jeff Leek490 • written 4.1 years ago by wrighth260
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gravatar for Jeff Leek
4.1 years ago by
Jeff Leek490
United States
Jeff Leek490 wrote:
Hi Hollis At the moment the only way you can perform these analyses is on a complete matrix of genomic measurements. Depending on the structure of the missing data, one approach is to use the impute package: http://www.bioconductor.org/packages/release/bioc/html/impute.html to impute the missing values before performing Combat/SVA. Hope this helps! Jeff On Mon, Sep 23, 2013 at 4:08 PM, Hollis Wright <wrighth@ohsu.edu> 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 > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 4.1 years ago by Jeff Leek490
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