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$byChipType(chipType,tags="coreR3,A20071112,EP")
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/HuEx-1_0-st-v2
Filename: HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf
Filesize: 38.25MB
Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 18708
Cells per unit: 350.31
Number of QC units: 1
> cs <- AffymetrixCelSet$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.
regards,
Mamun
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R version 2.11.1 (2010-05-31)
x86_64-unknown-linux-gnu
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] 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
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