Hi Jing, You have probably already figured this out by yourself already now, but extractDataFrame is what you are after. However it is meant to extract data from *subsets* of units, not for all units at the same time. Otherwise it is likely that you will run into memory problems. One thing you can do if you reall y need all this information in the same file is to use extractDataFrame on chunks of units and append each chunk to the file.
Hope this helps, Pierre. On Fri, Apr 24, 2009 at 9:56 AM, jing ma <jing...@gmail.com> wrote: > Dear Henrik, > > I'm analyzing some Affy SNP 6.0 array data and I followed the tutorial > "Total Copy Number Analysis (5.0 & 6.0)". I did all the steps from > "low-level analysis" till "PCR fragment length normalization" and stopped > at: > > fln <- FragmentLengthNormalization(ces) > cesN <- process(fln, verbose=verbose) > > Now, I want to output all the preprocessed and normalized signal estimates > for each marker (SNP and CN, totally 1881415 of them) in each sample in the > following format: > > MarkerID Chromosome Position sampleID-1 sampleID-2 ... sampleID-m > > > What functions should I use (extractMatrix or extractDataFrame or...) to > have all the above information? > > Thanks very much for your time! > > Jing > > Jing Ma > St. Jude Children's Research Hospital > > > > --~--~---------~--~----~------------~-------~--~----~ When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
