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

[Björn Usadel]

Dear Gordon,

thanks for you reply. Using your fix flush =TRUE did the trick.
Having it by default or adding a second warning in the help, would -at 
least for me- be good, since when reading a batch of arrays with one 
being broken can have some strange side-effects.
Apart from that, for my own purposes I added a perl script to validate 
the files, before using.

Kind regards,
Björn

Gordon Smyth wrote:
> Dear Bjoern,
> 
>> Date: Mon, 31 Jul 2006 12:43:00 +0200
>> From: Bj?rn Usadel <usadel at mpimp-golm.mpg.de>
>> Subject: [BioC] limma: read.maimages possibility to warn the user?
>> To: bioconductor at stat.math.ethz.ch
>>
>> 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
> 
> This unfortunate behaviour is due to (what I believe to be) a bug in the 
> R function read.table. (I've sent a post to R-devel today to discuss 
> it.) You can prevent it simply by adding the argument flush=TRUE to your 
> read.maimages() call. This will result in the spurious delimiters at the 
> of the end of the lines being ignored.
> 
> Perhaps I will add flush=TRUE to the limma read by default.
> 
>> 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"
> 
> This is something of an accident. If there had been five extra tab 
> characters at the end of the line instead of two, then marray would have 
> done exactly the same as limma. The difference between the two packages 
> is that limma is using fill=TRUE in the read while marray is not. This 
> allows limma to read incomplete lines.
> 
> Best wishes
> Gordon
> 
>> 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,
>> Bj?rn
>>
>>
>> -- 
>> -+-+-+-+-+-+-+-+-+-+-+-
>> Bj?rn Usadel, PhD
>>
>> Max Planck Institute of Molecular Plant Physiology
>> System Regulation Group
>>
>> Am M?hlenberg 1
>> D-14476 Golm
>> Germany
>>
>> Tel    (+49 331) 567-8114
>>
>> Email  usadel at mpimp-golm.mpg.de
>> WWW    mapman.mpimp-golm.mpg.de
> 

-- 
-+-+-+-+-+-+-+-+-+-+-+-
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