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

[James W. MacDonald]

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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