[BioC] gcrma background correction

[Sucheta Tripathy]

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_MEASUREMENT=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