[BioC] warning (condition has length>1) when reading in Agilent hyb text files

[John Fernandes]

Updating to the latest version of R and limma got rid of the error.  Thanks 
for the reply.

John

----- Original Message ----- 
From: "Herve Pages" <hpages at fhcrc.org>
To: "John Fernandes" <jfernand at stanford.edu>
Cc: "bioconduct" <bioconductor at stat.math.ethz.ch>
Sent: Friday, June 15, 2007 12:40 PM
Subject: Re: [BioC] warning (condition has length>1) when reading in Agilent 
hyb text files


Hi John,

limma 2.9.17 is old and this problem seems to have been fixed in more recent 
versions
of limma:

  hpages at lamb1:~/svn/Rpacks-2.1/limma/R> svn log -v -r 24408
  ------------------------------------------------------------------------
  r24408 | smyth at wehi.edu.au | 2007-04-30 21:17:31 -0700 (Mon, 30 Apr 2007) 
| 5 lines
  Changed paths:
     M /trunk/madman/Rpacks/limma/DESCRIPTION
     M /trunk/madman/Rpacks/limma/R/read-maimages.R
     M /trunk/madman/Rpacks/limma/inst/doc/changelog.txt

  1 May 2007: limma 2.11.1

  - Bug fix to read.columns() to stop spurious warning message
    when text.to.search has length greater than one.

  ------------------------------------------------------------------------

I recommend you update your limma package. Also you could update to R 2.5.0 
and
Bioconductor 2.0: many things have changed between BioC 1.9 and BioC 2.0 and 
a lot of
bugs have been fixed ;-)

Cheers,
H.


John Fernandes wrote:
> Anyone have an idea what could be causing the warning I'm getting?  Do
> you need more info from me?  Can I look up the error somewhere?
>
> Thanks,
> John
>
>
>> I'm reading Agilent text files generated from Feature Extractor 9.5.3 
>> into
>> limma with the following:
>>
>>     myfunFE <- function(x) {
>>         okAboveBG <- x[,"rIsWellAboveBG"]==1 & x[,"gIsWellAboveBG"]==1
>>         okSaturated <- x[,"rIsSaturated"]==0 & x[,"gIsSaturated"]==0
>>         okPopnOutlier <- x[,"rIsFeatPopnOL"]==0 & x[,"gIsFeatPopnOL"]==0
>>         okNonUnifOutlier <- x[,"rIsFeatNonUnifOL"]==0 &
>> x[,"gIsFeatNonUnifOL"]==0
>>         as.numeric(okAboveBG & okSaturated & okPopnOutlier &
>> okNonUnifOutlier)
>>     }
>>
>>     RG <- read.maimages(targets$FileName,path=hybpath,source="agilent",
>>
>> columns=list(Rf="rMedianSignal",Gf="gMedianSignal",Rb="rBGMedianSignal",Gb="gBGMedianSignal"),
>>     other.columns=othercols,wt.fun=myfunFE)
>>
>> I am getting a warning for each file:
>>
>>     "the condition has length > 1 and only the first element will be used
>> in: if (text.to.search != "") for (i in 1:ncn)"
>>
>>
>> However, I am getting results from the weight function.  Does the warning
>> indicate a problem?
>>
>> I am running R 2.4.1 on Win XP with limma 2.9.17.
>>
>> Thanks,
>> John Fernandes
>>
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