[BioC] limma: read.maimages possibility to warn the user?

[Björn Usadel]

Dear list,

when using read.maimages from limma with a "broken" file (tabs replaced 
by ":", two extra tabs added at the end of row e)
limma reads the table fine

table:
:R:G:RB:GB
a:1:2:0.5:0.5
b:2:4:1:1
c:3:6:1.5:1.5
d:4:8:2:2
e:5:10:2.5:2.5::
f:6:12:3:3
g:7:14:3.5:3.5

code:
RG<-read.maimages(files="test.txt", path="C://cpan//",columns=list(Gf="G",
                                            Rf="R",
                                            Gb="GB",
                                            Rb="RB"
                                            ))

But I get NA values added in all columns thus changing the order of 
probes in this particular arrayfile
$G
      test
[1,]    2
[2,]    4
[3,]    6
[4,]    8
[5,]   10
[6,]   NA  <-
[7,]   12
[8,]   14

Marray on the other hand, complains using the following syntax and 
refuses to read in the offending file.
RG2<-read.marrayRaw(fnames="test.txt",path="C://cpan//", name.Gf="G",
                                            name.Rf="R",
                                            name.Gb="GB",
                                            name.Rb="RB"
                                            )

"Error in scan(file = file, what = what, sep = sep, quote = quote, dec = 
dec,  :   line 5 did not have 5 elements"

Even though I appreciate, that limma reads the data fine without the 
usual read.table hazzle and realize that the data should have been 
checked before reading it in anyway, I think at least a little warning 
could greatly help.
But maybe I missed something important (not being a two color type anyway)?

(The broken files result from an MS Excel export and this happens on 
R2.2 with limma 2.4.13 and on R 2.3.1 with limma 2.6.2)


Cheers,
Björn


-- 
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Björn Usadel, PhD

Max Planck Institute of Molecular Plant Physiology
System Regulation Group

Am Mühlenberg 1
D-14476 Golm
Germany

Tel    (+49 331) 567-8114

Email  usadel at mpimp-golm.mpg.de
WWW    mapman.mpimp-golm.mpg.de