Combat generating negative values, should I log2 transform first?
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Entering edit mode
Ahdee ▴ 50
@ahdee-8938
Last seen 9 weeks ago
United States

Hi All,

I've been using the combat function from the SVA module to try and correct a batch effect. I have two groups but was however done at different time points.   here is an example of how I did it. I first dummy coded time into 1 and 2 and called this timebatch.

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pheno1<-read.table(file='batchfile.csv',sep=',')
batch=pheno1$timebatch modcombat = model.matrix(~1, data=pheno1) combat_edata = ComBat(dat=RAWsignal, batch=timebatch, mod=modcombat, par.prior=TRUE, prior.plots=FALSE) ------------------------------------------------------------------------------------------ this works however it produces negative results in some of the cells and as such I cannot log2 transform some of the rows. My question is should I log2 transform first then use the Combat function, and then quantile normalize, follow by a a linear design with limma? Is this appropriate or is there something else I can do? thanks in advance. Ahdee combat batch effect • 3.5k views ADD COMMENT 1 Entering edit mode @w-evan-johnson-5447 Last seen 2.0 years ago United States Ahdee, Its probably best to use ComBat on logged data. ComBat assumes that the data symmetric and bell-shaped. If you are still getting negative values, you can set anything negative to 0. Evan On Oct 12, 2015, at 8:13 PM, Ahdee [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""/> User Ahdee<https: support.bioconductor.org="" u="" 8938=""/> wrote Question: Combat generating negative values, should I log2 transform first?<https: support.bioconductor.org="" p="" 73266=""/>: Hi All, I've been using the combat function from the SVA module to try and correct a batch effect. I have two groups but was however done at different time points. here is an example of how I did it. I first dummy coded time into 1 and 2 and called this timebatch. ------------------------------------------------------------------------------------------ pheno1<-read.table(file='batchfile.csv',sep=',') batch=pheno1$timebatch modcombat = model.matrix(~1, data=pheno1) combat_edata = ComBat(dat=RAWsignal, batch=timebatch, mod=modcombat, par.prior=TRUE, prior.plots=FALSE) ------------------------------------------------------------------------------------------ this works however it produces negative results in some of the cells and as such I cannot log2 transform some of the rows. My question is should I log2 transform first then use the Combat function, and then quantile normalize, follow by a a linear design with limma? Is this appropriate or is there something else I can do? thanks in advance. Ahdee ________________________________ Post tags: combat, batch effect You may reply via email or visit Combat generating negative values, should I log2 transform first?
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