[BioC] Empty featureData in ExpressionSet generated by affy::justRMA

[David Shih]

Hi Jim,

Thank you for clarifying the purpose of the featureData slot.
The assayData slot also appears empty in my ExpressionSet.

The rownames are missing in my expression matrix extracted using.
> exprs(eset)

I was hoping to fill the rownames of my matrix using keys obtained
from
> keys <- mappedkeys(hgu133a2ACCUM)

I checked that all the keys are mapped, and I am under the impression
that they should be for hgu133a2ACCUM.

My main concern is that hgu133a2ACCUM may not return the keys
(probe ids) in the same order as they appear in the expression matrix,
which would cause the probes to be incorrectly mapped.

I have no problem with normalizing older platforms like U133. All the
probe ids are automatically assigned upon extraction with exprs().
However, the hthgu133a platform does not appear to be as
straightforward.

I had a similar problems with the HT Human Gene 1.0 ST platform.
I ended up using the oligo package, whicih provides a getNetAffx()
function to retrieve probe annotation data.
However, the existing normalization code precludes from switching to
the oligo package.

Best regards,
David

On Wed, May 18, 2011 at 01:51:01PM -0400, James W. MacDonald wrote:
> Hi David,
> 
> On 5/18/2011 1:31 PM, David Shih wrote:
> >Dear list,
> >
> >I am using the affy package to normalize expression data on the HT
> >Human Genome U133A platform. According to earlier posting on the list,
> >this is equivalent to U133Av2.
> >
> >I used the justRMA() function to normalize the data, and obtained an
> >ExpressionSet object with an empty featureData slot.
> 
> You may be misunderstanding the purpose of the featureData slot.
> According to ?eSet-class:
> 
> 'featureData': Contains variables describing features (i.e., rows
>           in 'assayData') unique to this experiment. Use the
>           'annotation' slot to efficiently reference feature data
>           common to the annotation package used in the experiment.
>           Class: 'AnnotatedDataFrame-class'
> 
> The probeset IDs are not unique to any particular experiment, so are
> stored as part of the assayData, which can be extracted using e.g.,
> exprs():
> 
> > data(sample.ExpressionSet)
> > head(exprs(sample.ExpressionSet))
>                        A         B        C        D        E
> F       G
> AFFX-MurIL2_at  192.7420  85.75330 176.7570 135.5750 64.49390
> 76.3569 160.5050
> AFFX-MurIL10_at  97.1370 126.19600  77.9216  93.3713 24.39860
> 85.5088 98.9086
> AFFX-MurIL4_at   45.8192   8.83135  33.0632  28.7072  5.94492
> 28.2925 30.9694
> AFFX-MurFAS_at   22.5445   3.60093  14.6883  12.3397 36.86630
> 11.2568 23.0034
> AFFX-BioB-5_at   96.7875  30.43800  46.1271  70.9319 56.17440
> 42.6756 86.5156
> AFFX-BioB-M_at   89.0730  25.84610  57.2033  69.9766 49.58220
> 26.1262 75.0083
> 
> Best,
> 
> Jim
> 
> 
> >
> >I understand that I can retrive the annotation information from:
> >library(hgu133a2.db)
> >
> >However, I am uncertain whether the probes in the annotation library
> >are in the same order as the ExpressionSet object.
> >
> >Can I add the probe IDs using the following code?
> >
> >library(hgu133a2.db)
> >keys<- mappedkeys(hgu133ai2ACCNUM);
> >expr<- exprs(eset);
> >rownames(expr)<- keys;
> >
> >
> >Best regards,
> >
> >David Shih, Graduate Student
> >The Hospital for Sick Children
> >Brain Tumour Research Centre
> >101 College Street, TMDT-11-401M
> >Toronto, ON  M5G1L7
> >Canada
> >Tel:  416-813-7654 x4327
> >
> >
> >>sessionInfo()
> >R version 2.12.2 (2011-02-25)
> >Platform: x86_64-unknown-linux-gnu (64-bit)
> >
> >locale:
> >  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> >  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> >  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
> >  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> >  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> >[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >
> >attached base packages:
> >[1] stats     graphics  grDevices utils     datasets  methods   base
> >
> >other attached packages:
> >[1] hgu133a2.db_2.4.5    org.Hs.eg.db_2.4.6   RSQLite_0.9-4
> >[4] DBI_0.2-5            AnnotationDbi_1.12.0 hthgu133acdf_2.7.0
> >[7] affy_1.28.0          Biobase_2.10.0
> >
> >loaded via a namespace (and not attached):
> >[1] affyio_1.18.0         preprocessCore_1.12.0 tools_2.12.2
> >
> >_______________________________________________
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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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