I have seen the problem. The CEL files I got is not binary file but begin like this: ------------------------------------ [CEL] Version=3
[HEADER] Cols=2560 Rows=2560 TotalX=2560 TotalY=2560 OffsetX=0 OffsetY=0 ----------------------------- What I need to do is to convert it to binary using convertCel(), is that so? Thanks Xinjun On Tue, Apr 21, 2009 at 2:56 PM, Mark Robinson <mrobin...@wehi.edu.au> wrote: > > > I still don't know what you mean by "directly processed" or "process > this raw file" because you haven't mentioned what you have tried or > what you are trying to do. > > Perhaps you just want to read it in? You could look at readCel() > routine from the 'affxparser' package. > > Perhaps you can mention the GSE number. Is there something wrong with > what you've downloaded, or something wrong with what is available to > download? > > Cheers, > Mark > > > > On 21/04/2009, at 4:42 PM, liszt wrote: > >> >> Thanks for your information! I mean the CEL file which can be directly >> processed is about 66M, but the raw CEL file I have downloaded from >> GEO through GSE# is about 150M. So how can I process this raw file ? >> Thanks. >> >> >> On Apr 21, 2:22 pm, Mark Robinson <mrobin...@wehi.edu.au> wrote: >>> On 21/04/2009, at 4:02 PM, Xinjun Zhang wrote: >>> >>>> Hi, >>> >>>> I have downloadedrawCELfile from GEO. Every of them are about 150MB >>>> which can not be processed directly. I want to know how to pre- >>>> process >>>> this kind ofrawfile? Thanks! >>> >>> Hi Xinjun. >>> >>> When you say "pre-process", what is it exactly you want to do? >>> >>> What have you tried and not been able to do? >>> >>> aroma.affymetrixwas designed to do many operations where you do not >>> read all chips' entire data into memory at once, but the pre- >>> processing steps are somewhat dependent on what chip type you have >>> and >>> what you are planning to do with it. >>> >>> Have you read the group pages? >>> >>> http://groups.google.com/group/aroma-affymetrix/web >>> >>> Hope that helps. >>> >>> Mark >>> >>> >>> >>> ------------------------------ >>> Mark Robinson >>> Epigenetics Laboratory, Garvan >>> Bioinformatics Division, WEHI >>> e: m.robin...@garvan.org.au >>> e: mrobin...@wehi.edu.au >>> p: +61 (0)3 9345 2628 >>> f: +61 (0)3 9347 0852 >>> ------------------------------ >> > > > ------------------------------ > Mark Robinson > Epigenetics Laboratory, Garvan > Bioinformatics Division, WEHI > e: m.robin...@garvan.org.au > e: mrobin...@wehi.edu.au > p: +61 (0)3 9345 2628 > f: +61 (0)3 9347 0852 > ------------------------------ > > > > > > > > --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
