Dear all, Using aroma.affymetrix I have fitted a GLAD model and would like to extract the (relative) copy-numbers. Following the aroma-affymetrix website I did: # get cdf > chiptypes <- c("Mapping250K_Sty", "Mapping250K_Nsp") > cdf <- AffymetrixCdfFile$fromChipType(chiptypes[1]) # get cel > name <- "TestSty250K" > cs <- AffymetrixCelSet$fromName(name, chipType=chiptypes[1]) # correct for allelic cross talk > acc <- AllelicCrosstalkCalibration(cs) > csC <- process(acc, verbose=verbose) # quantile normalization > cs.ac <- AffymetrixCelSet$fromName(name, tags="ACC,-XY", chipType=chiptypes[1]) > ac.qn <- QuantileNormalizationcs.ac) > csCN <- process(ac.qn, verbose=verbose) # normalization for sequence effects > cesNList <- list() > fln <- FragmentLengthNormalization(ces) > cesNList[[chiptypes[1]]] <- process(fln, verbose=verbose) > cesN <- cesNList[[chiptypes[1]]] # fit GLAD model > glad <- GladModel(cesNList) > ce <- ChromosomeExplorer(glad) > process(ce, verbose=verbose) Since ChromosomeExplorer can use the copy numbers for display, my question is: How can now I extract the raw copy-numbers and the fitted copy-numbers from the fitted GLAD model "glad"? This is what I tried w/o success: > tmp <- getRawCnData(glad, cesNList) # Exception: Argument 'ceList' contains a non-ChipEffectFile: CnChipEffectSet What kind of list do I need here? Is this the correct method to use? Then I tried to extract the data from the files in directory "gladData": > tmp <- AffymetrixCelSet$fromName(name, tags="QN,ACC,-XY,RMA,A+B,FLN,-XY", chipType=chiptypes[1], paths=c("gladData")) # Exception: No files found: gladData/TestSty250K,QN,ACC,-XY,RMA,A+B,FLN,-XY/Mapping250K_Sty Interestingly, the files in "gladData/TestSty250K,QN,ACC,-XY,RMA,A+B,FLN,-XY/Mapping250K_Sty" do exist! What is the reason for this? P.S.: I can extract the raw copy-numbers manually as described on the web-site, but not the fitted (and raw) copy-numbers from glad. Thank you in advance Best regards Chrstian ============================================== Christian Stratowa, PhD Boehringer Ingelheim Austria Dept NCE Lead Discovery - Bioinformatics Dr. Boehringergasse 5-11 A-1121 Vienna, Austria Tel.: ++43-1-80105-2470 Fax: ++43-1-80105-2782 email: christian.stratowa at vie.boehringer-ingelheim.com

Please post your questions to the aroma.affymetrix mailing list and it will get answered there. -Henrik On Mon, Feb 25, 2008 at 7:01 AM, <christian.stratowa at="" vie.boehringer-ingelheim.com=""> wrote: > Dear all, > > Using aroma.affymetrix I have fitted a GLAD model and would like to extract > the (relative) copy-numbers. > > Following the aroma-affymetrix website I did: > # get cdf > > chiptypes <- c("Mapping250K_Sty", "Mapping250K_Nsp") > > cdf <- AffymetrixCdfFile$fromChipType(chiptypes[1]) > > # get cel > > name <- "TestSty250K" > > cs <- AffymetrixCelSet$fromName(name, chipType=chiptypes[1]) > > # correct for allelic cross talk > > acc <- AllelicCrosstalkCalibration(cs) > > csC <- process(acc, verbose=verbose) > > # quantile normalization > > cs.ac <- AffymetrixCelSet$fromName(name, tags="ACC,-XY", > chipType=chiptypes[1]) > > ac.qn <- QuantileNormalizationcs.ac) > > csCN <- process(ac.qn, verbose=verbose) > > # normalization for sequence effects > > cesNList <- list() > > fln <- FragmentLengthNormalization(ces) > > cesNList[[chiptypes[1]]] <- process(fln, verbose=verbose) > > cesN <- cesNList[[chiptypes[1]]] > > # fit GLAD model > > glad <- GladModel(cesNList) > > ce <- ChromosomeExplorer(glad) > > process(ce, verbose=verbose) > > Since ChromosomeExplorer can use the copy numbers for display, my question > is: > How can now I extract the raw copy-numbers and the fitted copy- numbers from > the fitted GLAD model "glad"? > > This is what I tried w/o success: > > tmp <- getRawCnData(glad, cesNList) > # Exception: Argument 'ceList' contains a non-ChipEffectFile: CnChipEffectSet > > What kind of list do I need here? > Is this the correct method to use? > > Then I tried to extract the data from the files in directory "gladData": > > tmp <- AffymetrixCelSet$fromName(name, tags="QN,ACC,-XY,RMA,A+B,FLN,-XY", > chipType=chiptypes[1], paths=c("gladData")) > # Exception: No files found: > gladData/TestSty250K,QN,ACC,-XY,RMA,A+B,FLN,-XY/Mapping250K_Sty > > Interestingly, the files in > "gladData/TestSty250K,QN,ACC,-XY,RMA,A+B,FLN,-XY/Mapping250K_Sty" do exist! > What is the reason for this? > > P.S.: I can extract the raw copy-numbers manually as described on the > web-site, but not the fitted (and raw) copy-numbers from glad. > > Thank you in advance > Best regards > Chrstian > > ============================================== > Christian Stratowa, PhD > Boehringer Ingelheim Austria > Dept NCE Lead Discovery - Bioinformatics > Dr. Boehringergasse 5-11 > A-1121 Vienna, Austria > Tel.: ++43-1-80105-2470 > Fax: ++43-1-80105-2782 > email: christian.stratowa at vie.boehringer-ingelheim.com > > _______________________________________________ > 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 >