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
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
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
