[BioC] gcrma background correction-saving output
sutripa at vbi.vt.edu
Thu Dec 7 23:03:59 CET 2006
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:
write.table(tmp1, file="out.txt", row.names=FALSE, col.names=FALSE, sep="\t")
I get the following 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.
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.
> 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
>> 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
>> 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)
>> attached base packages:  "splines" "tools" "methods" "stats"
>>  "utils" "datasets" "base"
>> other attached packages: soybeanprobe soybeancdf gcrma
>> matchprobes affy affyio "1.14.0" "1.12.0" "2.7.0"
>> "1.12.1" "1.0.0"
>> Sucheta Tripathy, Ph.D.
>> Virginia Bioinformatics Institute Phase-I
>> Washington street.
>> Virginia Tech.
>> Blacksburg,VA 24061-0447
>> Fax: (540) 231-2606
>> web page: http://staff.vbi.vt.edu/sutripa blog :
>> quick ref: http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> Search the archives: http://news.gmane.org/
Sucheta Tripathy, Ph.D.
Virginia Bioinformatics Institute Phase-I
Fax: (540) 231-2606
web page: http://staff.vbi.vt.edu/sutripa
blog : http://genomics-array.blogspot.com/
More information about the Bioconductor