[BioC] trouble with gcrma: bgcorrection

[Zhijin (Jean) Wu]

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/
>
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