Hello! I am trying to run combat on 4 data sets that I got from GEO and I get the following error: Reading Sample Information File Reading Expression Data File Found 4 batches Found 1 covariate(s) Found 337 Missing Data Values Standardizing Data across genes Error in solve.default(t(des) %*% des) : Lapack routine dgesv: system is exactly singular: U[3,3] = 0 I noticed it had "missing data values" and isolated the problem to the last 200 genes (12,100 good ones left), however I still get the following error when I run the data without the last genes: Reading Sample Information File Reading Expression Data File Found 4 batches Found 1 covariate(s) Standardizing Data across genes Error in ((dat - t(design %*% B.hat))^2) %*% rep(1/n.array, n.array) : non-conformable arguments Do you have any suggestions what the problem might be? I would very much appreciate your help. Thank You! Tatiana K. Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 13 specialties. Named to FORTUNE? Magazine's "100 Best Companies to Work For?" list eight years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

It's hard to know exactly without seeing your data and code, but chances are that your model matrix or other sample information does not contain the same number of samples (rows) as the expression data (if I recall correctly, ComBat expects samples in columns of the expression data, so the number of rows of the model matrix must equal the number of columns of the expression data and the length of the batch variable). HTH, Peter On Mon, Nov 4, 2013 at 10:28 AM, Kovyrshina, Tatiana <tkovyrshina at="" houstonmethodist.org=""> wrote: > Hello! > > I am trying to run combat on 4 data sets that I got from GEO and I get the following error: > > Reading Sample Information File > Reading Expression Data File > Found 4 batches > Found 1 covariate(s) > Found 337 Missing Data Values > Standardizing Data across genes > Error in solve.default(t(des) %*% des) : > Lapack routine dgesv: system is exactly singular: U[3,3] = 0 > > I noticed it had "missing data values" and isolated the problem to the last 200 genes (12,100 good ones left), however I still get the following error when I run the data without the last genes: > > Reading Sample Information File > Reading Expression Data File > Found 4 batches > Found 1 covariate(s) > Standardizing Data across genes > Error in ((dat - t(design %*% B.hat))^2) %*% rep(1/n.array, n.array) : > non-conformable arguments > > Do you have any suggestions what the problem might be? I would very much appreciate your help. > > Thank You! > Tatiana K. > > Houston Methodist. Leading Medicine. > > Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 13 specialties. Named to FORTUNE? Magazine's "100 Best Companies to Work For?" list eight years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist > > ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you. > > _______________________________________________ > 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