[BioC] [maSigPro] T.fit - Error in rownames(coefficients)

[Maciej Jończyk]

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

Mª José 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,
>
> María.
>
> --------------------------------------------------
> From: "Maciej Jończyk" <mjonczyk at biol.uw.edu.pl>
> Sent: Wednesday, November 10, 2010 3:37 PM
> To: <bioconductor at stat.math.ethz.ch>
> Cc: "Maciej Jończyk" <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 Jończyk, MSc
> > Department of Plant Molecular Ecophysiology
> > Institute of Plant Experimental Biology
> > Faculty of Biology, University of Warsaw
> > 02-096 Warszawa, Miecznikowa 1
> >
> >
> >
> > ___________________________________
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> >
> >
> >
> >
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>
>


Maciej Jończyk, MSc
Department of Plant Molecular Ecophysiology
Institute of Plant Experimental Biology
Faculty of Biology, University of Warsaw
02-096 Warszawa, Miecznikowa 1



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