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

[Maciej Jończyk]

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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