Hi,

You may need to use eSet object instead of 'AffyBatch'. So, use exprs(tmp1).

write.table(exprs(tmp1), file="out.txt", row.names=FALSE, col.names=FALSE,
sep="\t")

Hope, this helps!
Anbarasu

On 12/7/06, Sucheta Tripathy <sutripa@vbi.vt.edu> wrote:
>
> Dear List,
>
> Thanks to all who responded to my earlier question. While I can get going
> with reading multiple CEL files at a time for background correction, I
> would like to save the outputs of each CEL file as a separate text file.
> While I tried something like this to have the outputs as separate columns
> in one file:
>
> library(affy)
> library(gcrma)
> affinfo=compute.affinities("soybean")
> myDat <-ReadAffy()
> sessionInfo()
> tmp1=bg.adjust.gcrma(myDat,optical.correct=T,affinity.info=affinfo)
> write.table(tmp1, file="out.txt", row.names=FALSE, col.names=FALSE,
> sep="\t")
>
> I get the following error
>
> Error:
> -------
> Error in as.data.frame.default(x[[i]], optional = TRUE) :
>     cannot coerce class "AffyBatch" into a data.frame
>
> I hope somebody can help me with this.
>
> many thanks
>
> Sucheta
>
> On Wed, December 6, 2006 11:57 pm, Kasper Daniel Hansen wrote:
> > 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
> >>
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@stat.math.ethz.ch
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives: http://news.gmane.org/
> >> gmane.science.biology.informatics.conductor
> >
>
>
> --
> 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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>



-- 
Lourdusamy A Anbarasu
Dipartimento Medicina Sperimentale e Sanita Pubblica
Via Scalzino 3
62032 Camerino (MC)

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