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

[Mª José Nueda]

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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