Hi, I was testing the package inSilicoMerging, particularly to perform the COMBAT batch effect removal. The original paper http://www.biomedcentral.com/1471-2105/13/335 sort of advertises the package handles covariates. However there seems to be no way to tell the merge function which column of the phenoData should be treated as such. Looking at the code, the function inSilicoMerging:::design.mat() was clearly written with covariates in mind, but inSilicoMerging:::mergeCOMBAT() drops all columns from the original phenoData. Is this a bug or covariates are not supported? Or did I miss something? Thank you, Francois Lefebvre

Hi Fran?ois, I am sorry for the confusion. Indeed the package do not handle covariates, but we plan to integrate this in next release. In the meantime I suggest you to take a look at the BatchAdjust method in the latest SCAN.UPC package. Kind regards, Quentin De Clerck Le 28 avr. 2014 ? 20:34, Fran?ois Lefebvre <lefebvrf at="" gmail.com=""> a ?crit : > Hi, > > I was testing the package inSilicoMerging, particularly to perform the > COMBAT batch effect removal. > > The original paper > > http://www.biomedcentral.com/1471-2105/13/335 > > sort of advertises the package handles covariates. > > However there seems to be no way to tell the merge function which > column of the phenoData should be treated as such. Looking at the > code, the function inSilicoMerging:::design.mat() was clearly written > with covariates in mind, but inSilicoMerging:::mergeCOMBAT() drops all > columns from the original phenoData. Is this a bug or covariates are > not supported? Or did I miss something? > > Thank you, > > Francois Lefebvre > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor