Question: [maSigPro] T.fit - Error in rownames(coefficients)
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gravatar for Maciej Jończyk
8.9 years ago by
Maciej Jończyk720 wrote:
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
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ADD COMMENTlink modified 8.9 years ago by Mª José Nueda90 • written 8.9 years ago by Maciej Jończyk720
Answer: [maSigPro] T.fit - Error in rownames(coefficients)
0
gravatar for Mª José Nueda
8.9 years ago by
Spain
Mª José Nueda90 wrote:
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@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
ADD COMMENTlink written 8.9 years ago by Mª José Nueda90
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
ADD REPLYlink written 8.9 years ago by Maciej Jończyk720
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
ADD REPLYlink written 8.9 years ago by Maciej Jończyk720
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