Question: fRMA error when using exprs()
0
8.2 years ago by
SylvainBrohée50 wrote:
Dear all, I am quite new to the "affymetrix normalization data world" and until now, I was always normalizing my data using the good old RMA method. People in the wet lab I am collaborating with asked me to renormalize a set of data coming from different labs and I discovered the fRMA method which is certainly more suitable in that case. I am working on the mouse so I used the mouse4302frmavecs package. This is my script : rawdata <- ReadAffy(filenames = cel.files) eset.frma <- frma(rawdata, summarize = 'batch'); When I run this, everything seems OK (about 5-6 to run) until I run this command : eset.df <- exprs(eset.frma); which produces the following error Error in function (classes, fdef, mtable) : unable to find an inherited method for function "exprs", for signature "PLMset" and if I look at my eset.frma object, I get this Probe level linear model (PLMset) object size of arrays=1002x1002 cdf=Mouse430_2 (45101 probeset ids) number of samples=6 number of probesets=45101 number of chip level parameters for each probeset=6 annotation=mouse4302 PLMset settings Creating function: Preprocessing Background Correction=Error in if (object at model.description$preprocessing$background) { : argument is of length zero The only thing I'd like are the expression values of course. Any idea about the cause of the problem? Many thanks to all of you, Sylvain Broh?e
normalization frma • 594 views
modified 8.2 years ago • written 8.2 years ago by SylvainBrohée50
Answer: fRMA error when using exprs()
0
8.2 years ago by
SylvainBrohée50 wrote:
I did not say I found the solution but I reinstalled everything (R, Bioconductor and all the packages I needed) and now it seems to work. Thanks for your help. Sylvain Broh?e On Thursday, September 15, 2011 11:48:55 AM Sylvain Broh?e wrote: > Dear all, > > I am quite new to the "affymetrix normalization data world" and until now, I > was always normalizing my data using the good old RMA method. > > People in the wet lab I am collaborating with asked me to renormalize a set of > data coming from different labs and I discovered the fRMA method which is > certainly more suitable in that case. > > I am working on the mouse so I used the mouse4302frmavecs package. > > This is my script : > > rawdata <- ReadAffy(filenames = cel.files) > eset.frma <- frma(rawdata, summarize = 'batch'); > > When I run this, everything seems OK (about 5-6 to run) until I run this > command : > > eset.df <- exprs(eset.frma); > > which produces the following error > > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "exprs", for signature > "PLMset" > > and if I look at my eset.frma object, I get this > > Probe level linear model (PLMset) object > size of arrays=1002x1002 > cdf=Mouse430_2 (45101 probeset ids) > number of samples=6 > number of probesets=45101 > number of chip level parameters for each probeset=6 > annotation=mouse4302 > PLMset settings > Creating function: > Preprocessing > Background Correction=Error in if > (object at model.description$preprocessing$background) { : > argument is of length zero > > > The only thing I'd like are the expression values of course. > > Any idea about the cause of the problem? > > Many thanks to all of you, > > Sylvain Broh?e > > _______________________________________________ > 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 >
Sylvain, The error went away because when you reinstalled everything, you updated to the latest version of the frma package. The error you were seeing was due to an issue in an earlier version. Best, Matt On Thu, Sep 15, 2011 at 7:18 AM, Sylvain Broh?e <sbrohee at="" ulb.ac.be=""> wrote: > I did not say I found the solution but I reinstalled everything (R, > Bioconductor and all the packages I needed) and now it seems to work. > > Thanks for your help. > > Sylvain Broh?e > > > On Thursday, September 15, 2011 11:48:55 AM Sylvain Broh?e wrote: >> Dear all, >> >> I am quite new to the "affymetrix normalization data world" and until now, I >> was always normalizing my data using the good old RMA method. >> >> People in the wet lab I am collaborating with asked me to renormalize a set > of >> data coming from different labs and I discovered the fRMA method which is >> certainly more suitable in that case. >> >> I am working on the mouse so I used the mouse4302frmavecs package. >> >> This is my script : >> >> rawdata <- ReadAffy(filenames = cel.files) >> eset.frma <- frma(rawdata, summarize = 'batch'); >> >> When I run this, everything seems OK (about 5-6 to run) until I run this >> command : >> >> eset.df <- exprs(eset.frma); >> >> which produces the following error >> >> Error in function (classes, fdef, mtable) ?: >> ? unable to find an inherited method for function "exprs", for signature >> "PLMset" >> >> and if I look at my eset.frma object, I get this >> >> Probe level linear model (PLMset) object >> size of arrays=1002x1002 >> cdf=Mouse430_2 (45101 probeset ids) >> number of samples=6 >> number of probesets=45101 >> number of chip level parameters for each probeset=6 >> annotation=mouse4302 >> PLMset settings >> Creating function: >> Preprocessing >> Background Correction=Error in if >> (object at model.description$preprocessing$background) { : >> ? argument is of length zero >> >> >> The only thing I'd like are the expression values of course. >> >> Any idea about the cause of the problem? >> >> Many thanks to all of you, >> >> Sylvain Broh?e >> >> _______________________________________________ >> 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 >> > > _______________________________________________ > 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 > -- Matthew N McCall, PhD 112 Arvine Heights Rochester, NY 14611 Cell: 202-222-5880