[BioC] [maSigPro] Error in T.fit - NAs introduced by coercion

[Maria Jose Nueda]

Dear Maciej,

This warning is not a problem.
The output of T.fit function is a list. One object of this list, named 
"sol", contains the p-vaules of the variables that the stepwise strategy 
decides to include in the model. So the variables that are not considered 
don't have any p-value to show and we decided to put "NA". Doing this R 
always show this warning, but for maSigPro this is not an error, it is 
normal.

Regards,

María José Nueda.


----- Original Message ----- 
From: "Maciej Jończyk" <mjonczyk at biol.uw.edu.pl>
To: <bioconductor at stat.math.ethz.ch>
Cc: "Maciej Jończyk" <mjonczyk at biol.uw.edu.pl>
Sent: Wednesday, April 28, 2010 10:47 PM
Subject: [BioC] [maSigPro] Error in T.fit - NAs introduced by coercion


> Dear list Members,
>
> I use maSigPro package, in T.fit I've got following warning message:
>
> There were 50 or more warnings (use warnings() to see the first 50)
>> warnings()
> Warning messages:
> 1: In rbind(sol, as.numeric(c(p.value, result$r.squared,  ... :
>  NAs introduced by coercion
> 2: In rbind(sol, as.numeric(c(p.value, result$r.squared,  ... :
>  NAs introduced by coercion
> ...
>
> I've searched the archive and I found that warning message containing
> "NAs introduced by coercion" happens also in other functions.
>
> Is it problem with coercion of data to matrix, i.e. command takes
> character column as a numeric one? My data desn't have NAs.
>
> Input to this command (T.fit) is an output of previous steps in ordinary
> maSigPro workflow (without errors/warnings), so I think data itself is
> correct.
>
> I'm not very experienced in programming and maybe there is an easy
> solution.
> I would like to ask for advice.
> Is it a serious warning (in object created in T.fit indeed are NAs)? Can
> I do something to avoid it?
>
> Here is my session info (two, because I run analysis on two computers
> and problem appears on both).
>
>> sessionInfo()
> R version 2.11.0 (2010-04-22)
> i486-pc-linux-gnu
>
> locale:
> [1] LC_CTYPE=pl_PL.UTF-8       LC_NUMERIC=C
> [3] LC_TIME=pl_PL.UTF-8        LC_COLLATE=pl_PL.UTF-8
> [5] LC_MONETARY=C              LC_MESSAGES=pl_PL.UTF-8
> [7] LC_PAPER=pl_PL.UTF-8       LC_NAME=C
> [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=pl_PL.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] tcltk     stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] maSigPro_1.20.0    DynDoc_1.26.0      widgetTools_1.26.0
> Biobase_2.8.0
>
> loaded via a namespace (and not attached):
> [1] limma_3.4.0      Mfuzz_2.6.0      tkWidgets_1.26.0
>
>
>
>> sessionInfo()
> R version 2.10.0 (2009-12-14)
> x86_64-pc-linux-gnu
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] tcltk     stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] maSigPro_1.18.0    DynDoc_1.24.0      widgetTools_1.24.0
> Biobase_2.6.1
>
> loaded via a namespace (and not attached):
> [1] limma_3.2.3      Mfuzz_2.4.0      tkWidgets_1.24.0
>
>
>
> Best Regards,
>
> 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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