[BioC] gcrma background correction

[Kasper Daniel Hansen]

Most likely this is a bug coming from the fact that a matrix with 1  
row (or column) usually gets silently changed to a vector. I am just  
guessing based on the fact that it only seems to happen with 1 chip.  
You are only doing background adjusting which should work ok with  
only one chip - a full GCRMA with multichip summarization would not  
make a whole lot of sense with 1 chip.

Kasper

On Dec 5, 2006, at 10:05 PM, Sucheta Tripathy wrote:

> Hi Jean, List,
>
> Finally I managed to make the script
>
> library(affy)
> library(gcrma)
> affinfo=compute.affinities("soybean")
> myDat <-ReadAffy()
> sessionInfo()
> tmp1=bg.adjust.gcrma(myDat,optical.correct=T,affinity.info=affinfo)
>
> run in my machine. The only thing I have noticed was it works with  
> 2 chips
> read simultaneously by ReadAffy(). For instance if I have only one CEL
> file instead of 2 CEL files in the working directory then I end up  
> having
> the same error that I used to get before. Is there a reason for that?
>
> Error Message:
> --------------
>
> 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 session info:
> ----------------
> 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_MESS
> AGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEA 
> SUREMENT=e
> n_US;LC_IDENTIFICATION=C
>
> 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"     "1.12.0"      "2.7.0"      "1.6.0"      
> "1.12.1"      "1.0.0"
>      Biobase
>     "1.12.2"
>
>
>
>
> 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/
> quick ref:
> http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/ 
> R_BioCondManual.html
>
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