Dear Maria, thanks for reply, I checked my input file and indeed there was few blank lines. I removed it, imported data to R and proceed as described earlier, problem remains. The problem must lie somewhere else because raw file (i.e. after reading to R) didn't cause problems in "p.vector" command. I encountered a problem in "T.fit" function, so i suppose that object generated by "p.vector" is invalid. Or this function is more susceptible to errors in input files than "p.vector" is, so the latter caused problems. Best Regards, Maciej M? Jos? Nueda <mj.nueda at="" ua.es=""> nadawca : > Dear Maciej, > > This error is related to the rownames of your data. Maybe there are > genes > without name. > > Regards, > > Mar?a. > > -------------------------------------------------- > From: "Maciej Jo?czyk" <mjonczyk at="" biol.uw.edu.pl=""> > Sent: Wednesday, November 10, 2010 3:37 PM > To: <bioconductor at="" stat.math.ethz.ch=""> > Cc: "Maciej Jo?czyk" <mjonczyk at="" biol.uw.edu.pl=""> > Subject: [BioC] [maSigPro] T.fit - Error in rownames(coefficients) > > > Dear list members, > > > > in T.fit function I've got following error message: > > > > Error in rownames(coefficients)[h] <- name : replacement has length > > zero > > > > I can't figure out what's wrong. > > I've been using maSigPro earlier and I didn't see this problem > > before. > > > > I use following code: > > > > >library("maSigPro") > > >dane5=read.table("cm50_2msp.txt",sep="\t",header=TRUE,fill=TRUE) > > > > # This data have missing values (blank fields) so I've used "fill" > > option. > > > > >des50=read.table("des50") > > >des5mx=as.matrix(des50) > > > > >design50=make.design.matrix(des5mx,degree=3) > > >fit5=p.vector(dane5,design50,Q=0.05,MT.adjust="BH") > > >fwdtw50=T.fit(fit5,step.method="two.ways.forward",alfa=0.05) > > > > >sessionInfo() > > > > R version 2.12.0 (2010-10-15) > > Platform: i486-pc-linux-gnu (32-bit) > > > > locale: > > [1] LC_CTYPE=pl_PL.utf8 LC_NUMERIC=C > > [3] LC_TIME=pl_PL.utf8 LC_COLLATE=pl_PL.utf8 > > [5] LC_MONETARY=C LC_MESSAGES=pl_PL.utf8 > > [7] LC_PAPER=pl_PL.utf8 LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=pl_PL.utf8 LC_IDENTIFICATION=C > > > > attached base packages: > > [1] tcltk stats graphics grDevices utils datasets > > methods > > [8] base > > > > other attached packages: > > [1] maSigPro_1.22.0 DynDoc_1.28.0 widgetTools_1.28.0 > > Biobase_2.10.0 > > > > loaded via a namespace (and not attached): > > [1] limma_3.6.6 Mfuzz_2.8.0 tkWidgets_1.28.0 > > > > > > Thank you, > > > > Maciej Jo?czyk, MSc > > Department of Plant Molecular Ecophysiology > > Institute of Plant Experimental Biology > > Faculty of Biology, University of Warsaw > > 02-096 Warszawa, Miecznikowa 1 > > > > > > > > ___________________________________ > > NOCC, http://nocc.sourceforge.net > > > > > > > > > > -- > > This email was Anti Virus checked by Astaro Security Gateway. > > http://www.astaro.com > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > Maciej Jo?czyk, MSc Department of Plant Molecular Ecophysiology Institute of Plant Experimental Biology Faculty of Biology, University of Warsaw 02-096 Warszawa, Miecznikowa 1 ___________________________________ NOCC, http://nocc.sourceforge.net

Dear Maria, I've figured out where problem lies - it was because I didn't specify column with row names in "read.table". Now it is ok. Thanks, Maciej M? Jos? Nueda <mj.nueda at="" ua.es=""> nadawca : > Dear Maciej, > > This error is related to the rownames of your data. Maybe there are > genes > without name. > > Regards, > > Mar?a. > > -------------------------------------------------- > From: "Maciej Jo?czyk" <mjonczyk at="" biol.uw.edu.pl=""> > Sent: Wednesday, November 10, 2010 3:37 PM > To: <bioconductor at="" stat.math.ethz.ch=""> > Cc: "Maciej Jo?czyk" <mjonczyk at="" biol.uw.edu.pl=""> > Subject: [BioC] [maSigPro] T.fit - Error in rownames(coefficients) > > > Dear list members, > > > > in T.fit function I've got following error message: > > > > Error in rownames(coefficients)[h] <- name : replacement has length > > zero > > > > I can't figure out what's wrong. > > I've been using maSigPro earlier and I didn't see this problem > > before. > > > > I use following code: > > > > >library("maSigPro") > > >dane5=read.table("cm50_2msp.txt",sep="\t",header=TRUE,fill=TRUE) > > > > # This data have missing values (blank fields) so I've used "fill" > > option. > > > > >des50=read.table("des50") > > >des5mx=as.matrix(des50) > > > > >design50=make.design.matrix(des5mx,degree=3) > > >fit5=p.vector(dane5,design50,Q=0.05,MT.adjust="BH") > > >fwdtw50=T.fit(fit5,step.method="two.ways.forward",alfa=0.05) > > > > >sessionInfo() > > > > R version 2.12.0 (2010-10-15) > > Platform: i486-pc-linux-gnu (32-bit) > > > > locale: > > [1] LC_CTYPE=pl_PL.utf8 LC_NUMERIC=C > > [3] LC_TIME=pl_PL.utf8 LC_COLLATE=pl_PL.utf8 > > [5] LC_MONETARY=C LC_MESSAGES=pl_PL.utf8 > > [7] LC_PAPER=pl_PL.utf8 LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=pl_PL.utf8 LC_IDENTIFICATION=C > > > > attached base packages: > > [1] tcltk stats graphics grDevices utils datasets > > methods > > [8] base > > > > other attached packages: > > [1] maSigPro_1.22.0 DynDoc_1.28.0 widgetTools_1.28.0 > > Biobase_2.10.0 > > > > loaded via a namespace (and not attached): > > [1] limma_3.6.6 Mfuzz_2.8.0 tkWidgets_1.28.0 > > > > > > Thank you, > > > > Maciej Jo?czyk, MSc > > Department of Plant Molecular Ecophysiology > > Institute of Plant Experimental Biology > > Faculty of Biology, University of Warsaw > > 02-096 Warszawa, Miecznikowa 1 > > > > > > > > ___________________________________ > > NOCC, http://nocc.sourceforge.net > > > > > > > > > > -- > > This email was Anti Virus checked by Astaro Security Gateway. > > http://www.astaro.com > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > Maciej Jo?czyk, MSc Department of Plant Molecular Ecophysiology Institute of Plant Experimental Biology Faculty of Biology, University of Warsaw 02-096 Warszawa, Miecznikowa 1 ___________________________________ NOCC, http://nocc.sourceforge.net