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

[Maciej Jończyk]

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

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
> >
> >
> >
> > ___________________________________
> > NOCC, http://nocc.sourceforge.net
> >
> >
> >
> >
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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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