
Dear List

I'm analyzing some (HumanHT12_V3_0_R1_11283641_A) Illumina data using the lumi package.  The raw data has 48803 probes, 36157 of which have a gene symbol annotation and 12646 don't.  When I use lumi, and convert probe ids to nuIDs, then annotate the nuIDs I only get 25935 probes annotated with a gene symbol.  

There can't be that many probes which have had annotated gene symbol deleted, so what am I doing wrong?
Is there a way to get the probe_ids and gene symbols that came with the raw data onto my TopTable post analysis?

My working below (not the full analysis just an example of how I did the annotation bit).

Thanks for you time.

John




> lumidata<-lumiR("Sample Probe Profile_rawdata.txt", lib.mapping='lumiHumanIDMapping')
Perform Quality Control assessment of the LumiBatch object ...
Duplicated IDs found and were merged!
> f <- exprs(lumidata)
> g<-as.matrix(rownames(f))
> f<-as.data.frame(cbind(f,g) )
> head(f)
                          1        2        3        4           V25
Ku8QhfS0n_hIOABXuE  92 84 75 79   Ku8QhfS0n_hIOABXuE
fqPEquJRRlSVSfL.8A 113  120 111 109  fqPEquJRRlSVSfL.8A
ckiehnugOno9d7vf1Q 107 104 94 94  ckiehnugOno9d7vf1Q 
x57Vw5B5Fbt5JUnQkI 93 83 94 94   x57Vw5B5Fbt5JUnQkI
ritxUH.kuHlYqjozpE 93 97 77 89  ritxUH.kuHlYqjozpE
QpE5UiUgmJOJEkPXpc 102 95 97  92  QpE5UiUgmJOJEkPXpc

> f$Symbol<-if (require(lumiHumanAll.db)) getSYMBOL(f$V25, 'lumiHumanAll.db')
> sum(is.na(f$Symbol))
[1] 22868


> data<-read.csv("Sample Probe Profile_rawdata.txt", header = TRUE, sep="\t")
> names(data)
  [1] "PROBE_ID"           "SYMBOL"             "X1.AVG_Signal"      
"X1.Detection.Pval"  "X1.NARRAYS"         "X1.ARRAY_STDEV"     "X1.BEAD_STDERR"    

    ...

> sum(is.na(data$SYMBOL))
[1] 0
> sum(data$SYMBOL=="")
[1] 12646
> sum(data$SYMBOL!="")
[1] 36157




> sessionInfo()
R version 2.10.1 (2009-12-14) 
i386-redhat-linux-gnu 

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=C             
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  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] beadarray_1.14.0         lumiHumanIDMapping_1.4.0 limma_3.2.3              lumi_1.12.4              MASS_7.3-4               preprocessCore_1.8.0    
 [7] mgcv_1.6-1               affy_1.24.2              lumiHumanAll.db_1.8.1    org.Hs.eg.db_2.3.6       RSQLite_0.8-4            DBI_0.2-5               
[13] annotate_1.24.1          AnnotationDbi_1.8.2      Biobase_2.6.1           

loaded via a namespace (and not attached):
 [1] affyio_1.14.0      grid_2.10.1        hwriter_1.2        KernSmooth_2.23-3  lattice_0.17-26    Matrix_0.999375-33 nlme_3.1-96       
 [8] tcltk_2.10.1       tools_2.10.1       xtable_1.5-6      
> 

 		 	   		  
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