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I've had GEO files get clipped early on me and come down fine if I asked for them in different ways, i.e. by asking for subsets which covered the whole set in different ways. Just look at the bottom of your cel files with an editor to see if they are complete. The diffs between Av2 and A can be seen at the bottom of the MAS5 output files ... one of them has about 25 extra probe sets. Tom ----- Original Message ----- From: "Adaikalavan Ramasamy" <ramasamy@cancer.org.uk> To: "weinong han" <hanweinong at="" yahoo.com=""> Cc: <bioconductor at="" stat.math.ethz.ch=""> Sent: Wednesday, July 13, 2005 6:06 AM Subject: Re: [BioC] problems of hgu95a >I had this problem before and I can think of two reasons > a) the file was somehow corrupted (e.g. during download). > b) the files do truly come from two different cel types > > It is easy to check b). Open up the cel files in notepad or a > spreadsheet. In the middle of line of line 18 or 19, you should see > something like "HG_U95Av2.1sq" which indicates that it is from HGU95av2. > Now repeat for a few CEL files. If it comes from two different types, > then you might want to double check with the authors. > > There is no need to go back to R-1.9.0 because I think you are going to > face the same problems and risk not getting updated packages. > > I believe that there is one extra probeset HGU95A and HGU95av2. I am > sure there must be other differences, otherwise Affy would not have > released a new version. Perhaps others on the list know. > > Regards, Adai > > > > On Tue, 2005-07-12 at 17:59 -0700, weinong han wrote: >> Dear All, >> >> I am analyzing Cromer A, Carles A et al. hypopharyngeal cancer data at >> various stages of progression. In their Oncogene paper (2004 Apr >> 1;23(14):2484-98), they mentioned they used hgu95a chip.When I loaded >> the all .cel files into R 2.1.0(OS:windows XP), I was told that: >> library(affy) >> Data <- ReadAffy() >> Error in initialize(value, ...) : Cel file D:/GSE2379_CEL/GSM44799.CEL >> does not seem to be of HG_U95Av2 type. >> >> Overall, 18 .cel files like GSM44799 do not seem to be of HG_U95Av2 type. >> >> Why happened so? I should go back to low version R like R1.9.0? What >> difference between HG_U95A and HG_U95Av2 type? >> >> How to fix it? >> >> please help me and thank you. >> >> >> >> >> >> Best Regards >> >> Han Weinong >> hanweinong at yahoo.com >> >> __________________________________________________ >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

I had this problem before and I can think of two reasons a) the file was somehow corrupted (e.g. during download). b) the files do truly come from two different cel types It is easy to check b). Open up the cel files in notepad or a spreadsheet. In the middle of line of line 18 or 19, you should see something like "HG_U95Av2.1sq" which indicates that it is from HGU95av2. Now repeat for a few CEL files. If it comes from two different types, then you might want to double check with the authors. There is no need to go back to R-1.9.0 because I think you are going to face the same problems and risk not getting updated packages. I believe that there is one extra probeset HGU95A and HGU95av2. I am sure there must be other differences, otherwise Affy would not have released a new version. Perhaps others on the list know. Regards, Adai On Tue, 2005-07-12 at 17:59 -0700, weinong han wrote: > Dear All, > > I am analyzing Cromer A, Carles A et al. hypopharyngeal cancer data at various stages of progression. In their Oncogene paper (2004 Apr 1;23(14):2484-98), they mentioned they used hgu95a chip.When I loaded the all .cel files into R 2.1.0(OS:windows XP), I was told that: > library(affy) > Data <- ReadAffy() > Error in initialize(value, ...) : Cel file D:/GSE2379_CEL/GSM44799.CEL does not seem to be of HG_U95Av2 type. > > Overall, 18 .cel files like GSM44799 do not seem to be of HG_U95Av2 type. > > Why happened so? I should go back to low version R like R1.9.0? What difference between HG_U95A and HG_U95Av2 type? > > How to fix it? > > please help me and thank you. > > > > > > Best Regards > > Han Weinong > hanweinong at yahoo.com > > __________________________________________________ > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >