[BioC] BeadArray: Associating a gene list file to probe summary data.

[Matt Ritchie]

Dear Cherie,

Try setting the 'ProbeID' argument in readBeadSummaryData() to "ProbeID"
instead of "TargetID".  The problem you have at the moment is that the
entries in "TargetID" are non-unique (caused by different beads targeting
the same transcript) so cannot be used as rownames of an 'exprs' object, and
are replaced by row numbers.  The ProbeIDs should be unique.

Then you can repeat your annotation with one of Lynn Amon's annotation
packages, which use the ProbeID as the key rather than the TargetID (see
http://article.gmane.org/gmane.science.biology.informatics.conductor/15288
I can send you the one relevant to your experiment off list if that would
help). 

Best wishes,

Matt

> Hi all,
> 
> I am very new to microarray analysis and bead arrays so please excuse me if
> this is a silly question.  I am attempting to associated the gene file for
> Mouse Ref 6 V1.1.  I am using the following code to load the summary file but
> I am unable to access the ProbeID information.
> 
> c.names=list(exprs = "AVG_Signal", NoBeads = "Avg_NBEADS",
> Detection="Detection", se.exprs ="BEAD_STDEV" ,Narrays="NARRAYS", arrayStDev =
> "ARRAY_STDEV")
> BSData = readBeadSummaryData(dataFile,skip=7, ProbeID="TargetID",
> columns=c.names)
> library(illuminaMousev1p1)
> illuminaMousev1p1()
> ids = rownames(exprs(BSData))
> chr = mget(ids, illuminaMousev1p1CHR,ifnotfound = NA)
> chrloc = mget(ids, illuminaMousev1p1CHRLOC,ifnotfound = NA)
> refseq = mget(ids, illuminaMousev1p1REFSEQ,ifnotfound = NA)
> genename = mget(ids, illuminaMousev1p1GENENAME,ifnotfound = NA)
> anno = cbind(Ill_ID = as.character(ids), Chr = as.character(chr), Loc =
> as.character(chrloc), RefSeq = as.character(refseq), Name =
> as.character(genename))
> ebFit$genes = anno
> topTable(ebFit)
> 
> R version 2.6.0 (2007-10-03)
> i386-pc-mingw32 
> 
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
>  [1] illuminaMousev1p1_1.2.0 lumi_1.4.0              mgcv_1.3-27
> beadarray_1.6.0         affy_1.16.0             preprocessCore_1.0.0
>  [7] affyio_1.6.1            geneplotter_1.16.0      lattice_0.16-5
> annotate_1.16.1         xtable_1.5-2            AnnotationDbi_1.0.6
> [13] RSQLite_0.6-3           DBI_0.2-4               Biobase_1.16.1
> limma_2.12.0            gplots_2.3.2            gdata_2.3.1
> [19] gtools_2.4.0
> 
> loaded via a namespace (and not attached):
> [1] grid_2.6.0         KernSmooth_2.22-21 RColorBrewer_1.0-2
> 
> 
>  When I use the "ids = rownames(exprs(BSData))" command the information I get
> is the row number not the ProbeID.  Am I doing something incorrectly?  Any
> help would be very much appreciated.
> 
> Thank you,
> Cherie