[BioC] oligo annotation: pd.mogene.2.0.st vs pd.mogene.2.0.st.v1

[Bernd Klaus]

Hi Jim,

thanks a lot for your prompt response!

Indeed, if I try

 oligo:::getCelChipType("/home/bernd/g/huber/users/klaus/Data/TinaRowold/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