Thanks a lot Anbarasu!! It does work. Just wanted to make sure if any values change in this conversion process? My output look little srange though. Anyway, thanks a lot. Sucheta On Fri, December 8, 2006 3:55 am, Lourdusamy A Anbarasu wrote: > 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 at="" 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=e >>>> n_ US;LC_MESS >>>> AGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_M >>>> EA >>>> 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 at 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 at 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) > > -- 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.htm l