Question: BiSeq - readBismark error
0
gravatar for Hans-Ulrich Klein
5.8 years ago by
United States
Hans-Ulrich Klein330 wrote:
Dear all, We would like to inform users of the BiSeq package, that there was in error in the readBismark() function that may - depending on the files and the order they were read in - lead to false methylation values. Affected BiSeq versions are 1.2.0 to 1.2.3. If you have used one of these versions to read in Bismark output, we suggest to update to version 1.2.4 and compare the obtained methylation values. I am really sorry for this. Best regards, Hans -- Dr. Hans-Ulrich Klein Institute of Medical Informatics University of M?nster Albert-Schweitzer-Campus 1 Geb?ude A11 48149 M?nster, Germany Tel.: +49 (0)251 83-58405
biseq • 922 views
ADD COMMENTlink modified 5.8 years ago by David Iles130 • written 5.8 years ago by Hans-Ulrich Klein330
Answer: BiSeq - readBismark error
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gravatar for David Iles
5.8 years ago by
David Iles130
David Iles130 wrote:
Hi, Thanks for the warning. When will the BiSeq 1.2.4 package be available? I?m about to start a methylation analysis ?. Dr David Iles Visiting Research Fellow School of Biology University of Leeds Leeds LS2 9JT UK d.e.iles at leeds.ac.uk<mailto:d.e.iles at="" leeds.ac.uk=""> On 5 Feb 2014, at 17:29, Hans-Ulrich Klein <h.klein at="" uni-="" muenster.de<mailto:h.klein="" at="" uni-muenster.de="">> wrote: Dear all, We would like to inform users of the BiSeq package, that there was in error in the readBismark() function that may - depending on the files and the order they were read in - lead to false methylation values. Affected BiSeq versions are 1.2.0 to 1.2.3. If you have used one of these versions to read in Bismark output, we suggest to update to version 1.2.4 and compare the obtained methylation values. I am really sorry for this. Best regards, Hans -- Dr. Hans-Ulrich Klein Institute of Medical Informatics University of M?nster Albert-Schweitzer-Campus 1 Geb?ude A11 48149 M?nster, Germany Tel.: +49 (0)251 83-58405 _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org<mailto:bioconductor at="" r-project.org=""> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 5.8 years ago by David Iles130
----- Original Message ----- > From: "David Iles" <d.e.iles at="" leeds.ac.uk=""> > To: "Hans-Ulrich Klein" <h.klein at="" uni-muenster.de=""> > Cc: bioconductor at r-project.org > Sent: Wednesday, February 5, 2014 10:00:32 AM > Subject: Re: [BioC] BiSeq - readBismark error > > Hi, > > Thanks for the warning. When will the BiSeq 1.2.4 package be > available? I?m about to start a methylation analysis ?. Assuming all goes well with the builds tonight, it should be available tomorrow morning around 11AM Seattle time. Dan > > Dr David Iles > Visiting Research Fellow > School of Biology > University of Leeds > Leeds LS2 9JT > UK > d.e.iles at leeds.ac.uk<mailto:d.e.iles at="" leeds.ac.uk=""> > > > > > > > On 5 Feb 2014, at 17:29, Hans-Ulrich Klein > <h.klein at="" uni-muenster.de<mailto:h.klein="" at="" uni-muenster.de="">> wrote: > > Dear all, > > We would like to inform users of the BiSeq package, that there was in > error in the readBismark() function that may - depending on the files > and the order they were read in - lead to false methylation values. > Affected BiSeq versions are 1.2.0 to 1.2.3. If you have used one of > these versions to read in Bismark output, we suggest to update to > version 1.2.4 and compare the obtained methylation values. I am > really > sorry for this. > > Best regards, > Hans > > -- > Dr. Hans-Ulrich Klein > Institute of Medical Informatics > University of M?nster > Albert-Schweitzer-Campus 1 > Geb?ude A11 > 48149 M?nster, Germany > Tel.: +49 (0)251 83-58405 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org<mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > 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 >
ADD REPLYlink written 5.8 years ago by Dan Tenenbaum8.2k
Hi David, I assme that the new version is going to be available within 24 hours. Of course, it is available on SVN already. Best, Katja David Iles schrieb am 2014-02-05: > Hi, > Thanks for the warning. When will the BiSeq 1.2.4 package be > available? I?m about to start a methylation analysis ?. > Dr David Iles > Visiting Research Fellow > School of Biology > University of Leeds > Leeds LS2 9JT > UK > d.e.iles at leeds.ac.uk<mailto:d.e.iles at="" leeds.ac.uk=""> > On 5 Feb 2014, at 17:29, Hans-Ulrich Klein > <h.klein at="" uni-muenster.de<mailto:h.klein="" at="" uni-muenster.de="">> wrote: > Dear all, > We would like to inform users of the BiSeq package, that there was in > error in the readBismark() function that may - depending on the files > and the order they were read in - lead to false methylation values. > Affected BiSeq versions are 1.2.0 to 1.2.3. If you have used one of > these versions to read in Bismark output, we suggest to update to > version 1.2.4 and compare the obtained methylation values. I am > really > sorry for this. > Best regards, > Hans > -- > Dr. Hans-Ulrich Klein > Institute of Medical Informatics > University of M?nster > Albert-Schweitzer-Campus 1 > Geb?ude A11 > 48149 M?nster, Germany > Tel.: +49 (0)251 83-58405 > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org<mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > _______________________________________________ > 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
ADD REPLYlink written 5.8 years ago by Katja Hebestreit10
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