oligo annotation: pd.mogene.2.0.st vs pd.mogene.2.0.st.v1
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Bernd Klaus ▴ 600
@bernd-klaus-6281
Last seen 3.8 years ago
Germany
Dear Jim, Dear Bioconductors, Jim, thanks a lot for providing the nice annotation packages for oligo! I have some mogene.2.0 microarray data and the cel files contain "MoGene-2_0-st-v1.1sq" as the chip identifier. So If I try to read them in using rawData <- read.celfiles(< list of celfiles > ) then oligo tries to download the "pd.mogene.2.0.st.v1" package, which does not exist. Can I just use rawData <- read.celfiles(< list of celfiles >, pkgname = "pd.mogene.2.0.st" ) ? After all it seems to be the same chip. What does the v1 mean anyway? Browsing the affymetrix website a bit seems to show that whenever you're looking at some technical documentation, it is called MoGene-2_0-st-v1, while in the datasheet pdf the v1 is left out ? Thanks a lot for your help! Bernd
Microarray Annotation oligo Microarray Annotation oligo • 1.4k views
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@james-w-macdonald-5106
Last seen 2 days ago
United States
Hi Bernd, I haven't seen that, but knowing Affymetrix I wouldn't be surprised if they changed some naming convention midstream. So here is what I get from some MoGene 2.0 ST arrays we ran about a year ago: > oligo:::getCelChipType("../CEL/M1.1 KO.CEL", TRUE) [1] "MoGene-2_0-st" And these of course expect a pd.mogene.2.0.st. If Affy changed some internal naming convention, then we will likely have to create both the pd.mogene.2.0.st and the pd.mogene.2.0.st.v1 packages. But I'll check with Benilton and see what he thinks. Thanks for the heads-up! Best, Jim On Thursday, April 03, 2014 4:54:08 AM, Bernd Klaus wrote: > Dear Jim, Dear Bioconductors, > > Jim, thanks a lot for providing the nice annotation packages > for oligo! > > I have some mogene.2.0 microarray data and the cel files contain > > "MoGene-2_0-st-v1.1sq" > > as the chip identifier. > > So If I try to read them in using > > rawData <- read.celfiles(< list of celfiles > ) > > then oligo tries to download the "pd.mogene.2.0.st.v1" > package, which does not exist. > > Can I just use > > rawData <- read.celfiles(< list of celfiles >, pkgname = "pd.mogene.2.0.st" ) ? > > After all it seems to be the same chip. > > What does the v1 mean anyway? > Browsing the affymetrix website a bit seems to show that whenever you're looking > at some technical documentation, it is called MoGene-2_0-st-v1, while in the datasheet > pdf the v1 is left out ? > > Thanks a lot for your help! > > Bernd -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Hi Jim, thanks a lot for your prompt response! Indeed, if I try oligo:::getCelChipType("/home/bernd/g/huber/users/klaus/Data/TinaRowo ld/RawData/KrasAll/KR2_MJRS_(MoGene-2_0-st).CEL", TRUE) I get "MoGene-2_0-st-v1" Best wishes, Bernd On Thu, 03 Apr 2014 10:55:26 -0400 "James W. MacDonald" <jmacdon at="" uw.edu=""> wrote: > Hi Bernd, > > I haven't seen that, but knowing Affymetrix I wouldn't be surprised if > they changed some naming convention midstream. So here is what I get > from some MoGene 2.0 ST arrays we ran about a year ago: > > > oligo:::getCelChipType("../CEL/M1.1 KO.CEL", TRUE) > [1] "MoGene-2_0-st" > > And these of course expect a pd.mogene.2.0.st. If Affy changed some > internal naming convention, then we will likely have to create both the > pd.mogene.2.0.st and the pd.mogene.2.0.st.v1 packages. > > But I'll check with Benilton and see what he thinks. > > Thanks for the heads-up! > > Best, > > Jim > > > > On Thursday, April 03, 2014 4:54:08 AM, Bernd Klaus wrote: > > Dear Jim, Dear Bioconductors, > > > > Jim, thanks a lot for providing the nice annotation packages > > for oligo! > > > > I have some mogene.2.0 microarray data and the cel files contain > > > > "MoGene-2_0-st-v1.1sq" > > > > as the chip identifier. > > > > So If I try to read them in using > > > > rawData <- read.celfiles(< list of celfiles > ) > > > > then oligo tries to download the "pd.mogene.2.0.st.v1" > > package, which does not exist. > > > > Can I just use > > > > rawData <- read.celfiles(< list of celfiles >, pkgname = "pd.mogene.2.0.st" ) ? > > > > After all it seems to be the same chip. > > > > What does the v1 mean anyway? > > Browsing the affymetrix website a bit seems to show that whenever you're looking > > at some technical documentation, it is called MoGene-2_0-st-v1, while in the datasheet > > pdf the v1 is left out ? > > > > Thanks a lot for your help! > > > > Bernd > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099
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