Dear All,

I am analysing some affymetrix exon array data. I have been performing some
Quality checking of the  data. I have extracted Transcript level RMA summarized
data.frame and produced a ExpressionSet object

I am using the core CDF file "HuEx-1_0-st-v2,coreR3,A20071112,EP"
developed by Elizabeth Purdom.

> chipType <- "HuEx-1_0-st-v2"
> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="coreR3,A20071112,EP")

> cdf
Path: annotationData/chipTypes/HuEx-1_0-st-v2
Filename: HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf
Filesize: 38.25MB
Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 18708
Cells per unit: 350.31
Number of QC units: 1

> cs <- AffymetrixCelSet$byName(exp_name,cdf=cdf)

> bc <- RmaBackgroundCorrection(cs, tag="coreR3")
> csBC <- process(bc,verbose=verbose)    ## Background corrected Raw Data

> ## *** summarization with PLM *** ##
> plmTr <- ExonRmaPlm(csBC, mergeGroups=TRUE)
> fit(plmTr, verbose=verbose)

> cesTr <- getChipEffectSet(plmTr)
> Tr_Data <- extractDataFrame(cesTr, units=NULL, addNames=TRUE)
> Tr_Expr<-as.matrix(Tr_Data[,6:dim(Tr_Data)[2]])
> TrExpSet <- new("ExpressionSet", exprs = Tr_Expr)

> featureNames(TrExpSet) <- Tr_Data$unitName
> TranscriptIds <- featureNames(TrExpSet)

Now I want this feature names (i.e. unitNames) to be tranlated to Gene Symbol,
Gene Name, Chr Location  using biomaRt. 

> listMarts()
> ensembl = useMart("ensembl")
> ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)

> r1 <- getBM(attributes = c("affy_huex_1_0_st_v2","hgnc_symbol"),     filters 
> = "affy_huex_1_0_st_v2", values = TranscriptIds, mart = ensembl)

It returns a data frame with 0 row and 0 column. 

Then doing some reading in the forum I found that since this CDF was based on 
NetAffx file and mapping using
biomaRt is possible via probeset Ids / group names. so far I could not find any 
way do the mapping from 
summarized transcript Ids to Gene name/symbol/.

So my questions are 

1. Is it possible to annotate unitNames (i.e Transcript ID ) to Gene symbol, 
name or Ref Seq using biomaRt ?

2. If answer to question 1 is NO,  then Can the annotation  be done with csv 
file  "HuEx-1_0-st-v2.r2.dt1.hg18.csv"
    via some R scripts. ??? 

3. If this restriction is because of the CDF file I am using, what CDF file 
suitable for annotation with e.g. ensembl ?
    I have there are some  ensembl CDF created by Elizabeth Purdom. If I use 
those CDF to process ( bc , norm, ) 
   and summarization (Transcript level ), will I have ENSEMBL IDs as Transcript 
ID. ??
Any help and suggestions are welcome.

Thanks in advance. and Have a nice Week end.


R version 2.11.1 (2010-05-31) 

 [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            

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] biomaRt_2.4.0          lumi_1.14.0            MASS_7.3-6            
 [4] RSQLite_0.9-1          DBI_0.2-5              mgcv_1.6-2            
 [7] annotate_1.26.0        AnnotationDbi_1.10.1   preprocessCore_1.10.0 
[10] Biobase_2.8.0          session_1.0.2          aroma.affymetrix_1.6.0
[13] aroma.apd_0.1.7        affxparser_1.20.0      R.huge_0.2.0          
[16] aroma.core_1.6.0       aroma.light_1.16.0     matrixStats_0.2.1     
[19] R.rsp_0.3.6            R.filesets_0.8.2       digest_0.4.2          
[22] R.cache_0.3.0          R.utils_1.4.2          R.oo_1.7.3            
[25] affy_1.26.1            R.methodsS3_1.2.0     

loaded via a namespace (and not attached):
[1] affyio_1.16.0      grid_2.11.1        lattice_0.18-8     Matrix_0.999375-39
[5] nlme_3.1-96        RCurl_1.4-2        tools_2.11.1       XML_3.1-0         
[9] xtable_1.5-6      

When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.

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