Hi Jun, Note that the ComBat user forum Google Group is closed. ComBat support should now go through the Bioconductor mailing list. Looking at your output, ComBat is detecting 49 batches. Is this true? Evan On Dec 7, 2013, at 10:32 AM, Jun Li wrote: Hi, I’m a user of ComBat function in sva package. We are adjusting batch effect in a methylation450k project. I met a problem recently when using ComBat and hope you could help me. I have used Combat for batch effect adjusting before (96 samples * 470078 probes) and the script ran well. However, recently, when we enlarged our sample size (206 samples) and ran the script again, an error occurred (as in attached file). I rechecked the data I prepared and the script for many times and I couldn’t figure out why. It will be really appreciated if you could help me with the problem. Sorry to bother you. I tried to get in the Combat-user-forum to ask but I have no authority. Thank you so much. Best wishes. Jun <combat_problem1.rout> [[alternative HTML version deleted]]

Hi, I have not been able to see the attached file. However, the high number of batches sometimes indicates that we have failed to indicate the continuous covariates (with the numCovs argument), thus taking a continuous variable as a factor... Could it be this? Regards, Gus El 09/12/13 15:54, Johnson, William Evan escribió: > Hi Jun, > > Note that the ComBat user forum Google Group is closed. ComBat support should now go through the Bioconductor mailing list. > > Looking at your output, ComBat is detecting 49 batches. Is this true? > > Evan > > > > On Dec 7, 2013, at 10:32 AM, Jun Li wrote: > > Hi, > > > > IâEUR^(TM)m a user of ComBat function in sva package. We are adjusting batch effect in a methylation450k project. I met a problem recently when using ComBat and hope you could help me. > I have used Combat for batch effect adjusting before (96 samples * 470078 probes) and the script ran well. However, recently, when we enlarged our sample size (206 samples) and ran the script again, an error occurred (as in attached file). I rechecked the data I prepared and the script for many times and I couldnâEUR^(TM)t figure out why. It will be really appreciated if you could help me with the problem. > Sorry to bother you. I tried to get in the Combat-user-forum to ask but I have no authority. > > > > Thank you so much. > > > > Best wishes. > Jun > > > <combat_problem1.rout> > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > 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]]