[BioC] How remove controls probes - Affymetrix Gene

[James W. MacDonald]

Hi Sophie,

On 1/12/2012 11:01 AM, Sophie Lamarre [guest] wrote:
> Hello,
>
> I work on affymetrix mouse gene 1.0 ST.
>
> I want to know how remove controls probes on Affymetrix Gene.
> In my studie, I downloaded two files on Affymetrix website:
> - The Probeset Annotations, CSV Format, Release 32
>   file (NetAffx Analysis Center ->  Exon/Gene ->  NetAffy Query ->  "Mouse Gene 1.0 ST")
> - The Transcript Cluster Annotations, CSV, Release 32 file (NetAffx Analysis Center ->  Exon/Gene ->  NetAffy Query ->  "Mouse Gene 1.0 ST")
>
> With the first, I had 28 856 main probesets and with second 28 350 main probesets.
>
> I add that I run a RMA option "core" with the oligo package. I just want a probe for a probeset.

I'm not sure what you are asking here. You can't have a probe for a 
probeset, as there are multiple probes in each probeset. The default for 
rma() in oligo is to summarize the probesets at the transcript level, 
which is in general what most people want. You can summarize at the 
'probeset' level, which is something like summarizing at the exon level, 
but if I am not mistaken, there can be more than one probeset per exon, 
so that gets complicated. Summarizing at the transcript level is an 
easier path to take.

>
> Which file I have to use? (I did'nt use the command getNetAffy because I realized that I lost more probesets! (There were only 28 270 main probes)).

Rather than getting annotation data from netaffx and then struggling 
with the format, it is easier to install the 
mogene10sttranscriptcluster.db package, and use that for annotating your 
data. There are vignettes in the AnnotationDbi package that show how to 
use that package.

Best,

Jim



>
> Thank you for advance for your answer and your help.
>
> Sophie LAMARRE
>
>   -- output of sessionInfo():
>
> R version 2.13.0 (2011-04-13)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252    LC_MONETARY=French_France.1252
> [4] LC_NUMERIC=C                   LC_TIME=French_France.1252
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>   [1] pd.mogene.1.0.st.v1_3.2.0 oligo_1.16.2              preprocessCore_1.14.0
>   [4] GOstats_2.18.0            RSQLite_0.9-4             DBI_0.2-5
>   [7] graph_1.30.0              Category_2.18.0           genefilter_1.34.0
> [10] gplots_2.8.0              caTools_1.12              bitops_1.0-4.1
> [13] gdata_2.8.2               gtools_2.6.2              geneplotter_1.30.0
> [16] lattice_0.19-23           annotate_1.30.0           AnnotationDbi_1.14.1
> [19] RColorBrewer_1.0-5        ArrayTools_1.12.0         affy_1.30.0
> [22] limma_3.8.3               oligoClasses_1.14.0       Biobase_2.12.2
>
> loaded via a namespace (and not attached):
>   [1] affxparser_1.24.0 affyio_1.20.0     Biostrings_2.20.3 bit_1.1-7         ff_2.2-3
>   [6] GO.db_2.5.0       GSEABase_1.14.0   IRanges_1.10.6    RBGL_1.28.0       splines_2.13.0
> [11] survival_2.36-5   tools_2.13.0      XML_3.4-2.2       xtable_1.5-6
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826

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