Are you using the 'sva' package version or the R script? On May 10, 2013, at 1:51 PM, Marc-Danie Jessica Nazaire wrote: Hi Igor, We are getting this error when running ComBat with no covariates specified (runs successfully with covariates) but there are no non- numeric or missing values in our dataset. I did some debugging and tracked down the error to this piece of code: if (!NAs){gamma.hat <- solve(t(batch.design)%*%batch.design)%*%t(batch .design)%*%t(as.matrix(s.data))}else{gamma.hat=apply(s.data,1,Beta.NA, batch.design)} NOTE: s.data and batch.design have no NAs The gamma.hat matrix has NAs after this calculation and fails later during the call: gamma.bar <- apply(gamma.hat, 1, mean) Do you have any more ideas or insights on what could be causing this error? Thanks, Marc-Danie On Tuesday, June 9, 2009 2:57:40 PM UTC-4, Evan wrote: If you see the "Error in FUN(newX[, i], ...) : missing observations in cov/cor" error message while running ComBat, search for non-numeric or missing values in your data file. It will work fine when you fixed them. Igor -- [[alternative HTML version deleted]]

No, I am not. Marc-Danie On Friday, May 10, 2013 1:57:50 PM UTC-4, Evan Johnson wrote: > > Are you using the 'sva' package version or the R script? > > > On May 10, 2013, at 1:51 PM, Marc-Danie Jessica Nazaire wrote: > > Hi Igor, > > We are getting this error when running ComBat with no covariates > specified (runs successfully with covariates) but there are no non- numeric > or missing values in our dataset. > > I did some debugging and tracked down the error to this piece of code: > if (!NAs){gamma.hat <- > solve(t(batch.design)%*%batch.design)%*%t(batch.design)%*%t(as.matri x(s.data))}else{gamma.hat=apply(s.data,1,Beta.NA,batch.design)} > > NOTE: s.data and batch.design have no NAs > > The gamma.hat matrix has NAs after this calculation and fails later during > the call: > gamma.bar <- apply(gamma.hat, 1, mean) > > > Do you have any more ideas or insights on what could be causing this > error? > > Thanks, > Marc-Danie > > On Tuesday, June 9, 2009 2:57:40 PM UTC-4, Evan wrote: >> >> If you see the "Error in FUN(newX[, i], ...) : missing observations in >> cov/cor" error message while running ComBat, search for non-numeric >> or >> missing values in your data file. It will work fine when you fixed >> them. >> >> Igor > > > -- > > >