[BioC] trouble with gcrma: bgcorrection

[Sucheta Tripathy]

Hi Jean,

Thanks for running it in your machine. I tried running the same thing in
another machine with freshly installed R with bioconductor and got the
same error as before. the only difference I see is you have gcrma 2.7.0
while mine is 2.6.0. Will this be the possible cause?

I looked at the distribution and found 2.6.0 to be the latest available
version. Do you have anything different?

Thanks

Sucheta

My Errors:
===========
> affinfo=compute.affinities("soybean")
Computing affinities.Done.
> myDat <- ReadAffy(filenames="C:/test_bg/49_C033.1B.R9B3L.CEL")
> sessionInfo()
R version 2.4.0 (2006-10-03)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] "splines"   "tools"     "methods"   "stats"     "graphics"  "grDevices"
[7] "utils"     "datasets"  "base"

other attached packages:
soybeanprobe   soybeancdf        gcrma  matchprobes         affy       affyio
    "1.14.0"     "1.14.0"      "2.6.0"      "1.6.0"     "1.12.1"      "1.2.0"
     Biobase
    "1.12.2"
> tmp1=bg.adjust.gcrma(myDat,optical.correct=T,affinity.info=affinfo)
Adjusting for optical effect.Done.
Error in model.frame(formula, rownames, variables, varnames, extras,
extranames,  :
        variable lengths differ (found for 'x')

===================================================

On Tue, November 28, 2006 9:35 pm, Zhijin (Jean) Wu wrote:
> Hi, Sucheta,
> I got your data and tested it. It runs fine on my machine
>
>
>> affinfo=compute.affinities("soybean")
> Computing affinities.
> Done.
>
>> tmp1=bg.adjust.gcrma(myDat,optical.correct=T,affinity.info=affinfo)
> Adjusting for optical effect..Done.
> Adjusting for non-specific binding..Done.
>
>> sessionInfo()
> R version 2.4.0 alpha (2006-09-06 r39158)
> sparc-sun-solaris2.9
>
> locale:
> C
>
>
> attached base packages: [1] "splines"   "tools"     "methods"   "stats"
> "graphics"
> "grDevices"
> [7] "utils"     "datasets"  "base"
>
>
> other attached packages: gcrma soybeanprobe  matchprobes         affy
> affyio Biobase
> "2.7.0"     "1.14.0"      "1.5.0"     "1.11.6"      "1.1.8"
> "1.13.2"
> soybeancdf "1.14.0"
>
>
> On Mon, 27 Nov 2006, Sucheta Tripathy wrote:
>
>
>>
>> Dear List,
>>
>>
>> I still have problem computing background correction with gcrma using
>> the following simpler code with soybean chip.
>>
>> library(affy) library(gcrma) myDat<-ReadAffy() myBG <-
>> bg.adjust.gcrma(myDat)
>>
>>
>> My error message is:
>> -------------------
>> Adjusting for optical effect.Done.
>> Computing affinities.Done.
>> Error in model.frame(formula, rownames, variables, varnames, extras,
>> extranames,  : variable lengths differ (found for 'x') Execution halted
>>
>> ---
>>
>>
>> my sessioninfo(): -----------------
>> R version 2.4.0 (2006-10-03)
>> i686-pc-linux-gnu
>>
>> locale:
>> LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=C;LC_MONETARY=en_US
>> ;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C
>> ;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C
>>
>>
>> attached base packages: [1] "methods"   "stats"     "graphics"
>> "grDevices" "utils"     "datasets"
>> [7] "base"
>> -------------------
>>
>>
>> Has anyone faced similar problem. I am stuck here and any help will be
>> greatly appreciated. This seemed to work well with the earlier versions
>> of R and soybeancdf.
>>
>>
>> Many thanks
>>
>>
>> Sucheta
>>
>>
>>
>>
>>
>>
>>
>> --
>> Sucheta Tripathy, Ph.D.
>> Virginia Bioinformatics Institute Phase-I
>> Washington street.
>> Virginia Tech.
>> Blacksburg,VA 24061-0447
>> phone:(540)231-8138
>> Fax:  (540) 231-2606
>>
>>
>> web page: http://staff.vbi.vt.edu/sutripa blog    :
>> http://genomics-array.blogspot.com/
>>
>>
>> _______________________________________________
>> Bioconductor mailing list
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>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>>
>>
>


-- 
Sucheta Tripathy, Ph.D.
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
phone:(540)231-8138
Fax:  (540) 231-2606

web page: http://staff.vbi.vt.edu/sutripa
blog    : http://genomics-array.blogspot.com/