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

[James W. MacDonald]

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