Hello! I am trying to run ComBat on 4 batches of colorectal cancer that I got from the GEO website. I had success before with ComBat with different files, but for these R keeps giving me an error message: >source("ComBat.R") > ComBat("output_file.txt","Sample Information File.txt") Reading Sample Information File Reading Expression Data File Found 5 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[1,1] = 0 I tried running it only on the first 100 genes, same problem. I tried only the first 10 genes, same problem. I tried using only 2 batches and same problem. I ran SCAN, but I cannot attach the output file from that because it is too big. I did attach my sample information file. Do you have any suggestions for me about what could be wrong? Thank You! Tatiana Kovyrshina 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. -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: Sample Information File.txt URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20131028="" 027e1e63="" attachment.txt="">

ComBat says it found 5 batches instead of 4. That's your hint - it seems your batch information is not read in correctly. Peter On Mon, Oct 28, 2013 at 9:22 AM, Kovyrshina, Tatiana <tkovyrshina at="" houstonmethodist.org=""> wrote: > Hello! > I am trying to run ComBat on 4 batches of colorectal cancer that I got from the GEO website. I had success before with ComBat with different files, but for these R keeps giving me an error message: > >>source("ComBat.R") >> ComBat("output_file.txt","Sample Information File.txt") > Reading Sample Information File > Reading Expression Data File > Found 5 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[1,1] = 0 > > I tried running it only on the first 100 genes, same problem. I tried only the first 10 genes, same problem. I tried using only 2 batches and same problem. I ran SCAN, but I cannot attach the output file from that because it is too big. I did attach my sample information file. > > Do you have any suggestions for me about what could be wrong? > > Thank You! > Tatiana Kovyrshina > > 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