Hi Markus, sorry but this one slipped through my net.
On Thu, Jun 17, 2010 at 5:27 PM, Smaug72 <leber.mar...@gmx.de> wrote: > Dear Henrik, > > unfortunately we are faced with another problem. > We processed several CEL files with CRMAv2 as decribed by vignette: > http://aroma-project.org/vignettes/CRMAv2 > We received no errors during the run. > > The problem is that we cannot process the CEL files, which are > generated. > > The CEL-Files generated in step 2 (Normalization for nucleotide- > position probe sequence effects) have a size of about 65,9 MB. > These files can be loaded by GTC Software version 4.0, but they cannot > be processed by further examination (e.g. QC-matrix calculation) Yes, the output of all *probe-level* preprocessing methods generates CEL files of the same format/layout that you can treat as if they were raw CEL files. You should be able to use these CEL files in for instance the Affymetrix GTC software, dChip and so on. > > The CEL files generated in step 3 (Probe summarization) have a size of > about 26,9 MB (decrease in size of about 39 MB). > These CEL-Files cannot by loaded by GTC Software version 4.0. No/correct, because those CEL files are so called chip-effect CEL files (*,chipEffects.CEL), which are custom-made (=only recognized) by the aroma.affymetrix software. They cannot be read by other software (and you should not try to either). It sounds like you wish to export the summarized CN signals from aroma.affymetrix into the Affymetrix GTC software. I don't know what kind of data GTC can import, but you can export/write CN signals to tab-delimited text files by: # CRMA v2 vignette cesN <- ... # from the PCR fragment-length normalization # Generate platform-independent data sets dsNList <- exportTotalAndFracB(cesN, drop=FALSE); Then you can do: writeDataFrame(dsNList$total, ...); and (only if you used combineAlleles=FALSE): writeDataFrame(dsNList$fracB, ...); For more details on writeDataFrame() and what is written, see http://aroma-project.org/howtos/writeDataFrame The data is (total,fracB) = (total signal, allele B fractions). If you want (thetaA,thetaB) or similar you need to fix that yourself afterward. Again, I don't know what kind of data Affymetrix GTC can import, if any. BTW, if you use doCRMAv2() it will do/return 'dsNList' for you, cf. http://aroma-project.org/blocks/doCRMAv2. That may be more convenient for you. Hope this helps Henrik > > Do have experience with this error or explanations? > > Thank you and best regards, > Markus > > -- > 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 with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > -- 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 with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
