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

[David Shih]

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.

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