On Sun, Mar 1, 2009 at 5:14 AM, Peter Robinson
<peter.robinson@t-online.de>wrote:

> Hi all,
>
> I am trying to use the affy package to analyze  GeneChip® Mouse Gene 1.0 ST
> Array data.  What do I need to do to get the CDF information for this chip?
> I am loading the
> mogene10st.db package, but that doesnt seem to be correct.
> Thanks a lot, Peter
>
> > library(affy)
> Lade nötiges Paket: Biobase
> Lade nötiges Paket: tools
>
> Welcome to Bioconductor
>
>  Vignettes contain introductory material. To view, type
>  'openVignette()'. To cite Bioconductor, see
>  'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> Lade nötiges Paket: affyio
> Lade nötiges Paket: preprocessCore
>
> > library(mogene10st.db)
> Lade nötiges Paket: AnnotationDbi
> Lade nötiges Paket: DBI
> > myAffy = ReadAffy(filenames=celfiles)
>
> > myAffy
> AffyBatch object
> size of arrays=1050x1050 features (11 kb)
> cdf=MoGene-1_0-st-v1 (??? affyids)
> number of samples=24
> Fehler in getCdfInfo(object) :
>  Could not obtain CDF environment, problems encountered:
> Specified environment does not contain MoGene-1_0-st-v1
> Library - package mogene10stv1cdf not installed
> Data for package affy did not contain mogene10stv1cdf
> Bioconductor - mogene10stv1cdf not available
> Zusätzlich: Warning message:
> missing cdf environment! in show(AffyBatch)
>
>
Hi, Peter.  The affy package will not work with ST arrays.  See this page
for options:

http://bioconductor.org/docs/workflows/oligoarrays/

Sean



>
> > sessionInfo()
> R version 2.8.1 (2008-12-22)
> i486-pc-linux-gnu
>
> locale:
> LC_CTYPE=de_DE@euro;LC_NUMERIC=C;LC_TIME=de_DE@euro;LC_COLLATE=de_DE@euro
> ;LC_MONETARY=C;LC_MESSAGES=de_DE@euro;LC_PAPER=de_DE@euro
> ;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE@euro
> ;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] mogene10st.db_1.0.2  RSQLite_0.6-4        DBI_0.2-4
> [4] AnnotationDbi_1.4.3  affy_1.18.2          preprocessCore_1.2.0
> [7] affyio_1.8.0         Biobase_2.0.1
>
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