[BioC] oligo annotation: pd.mogene.2.0.st vs pd.mogene.2.0.st.v1
bernd.klaus at embl.de
Thu Apr 3 17:33:16 CEST 2014
thanks a lot for your prompt response!
Indeed, if I try
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)
>  "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!
> 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.
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
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