After my premature posting yesterday, I am bit hesitant to ask, but I am 
puzzled by what I am getting from biomaRt.  (To avoid clutter, I added 
the sessionInfo at the end of the message.)

I used ReadAffy() to read in a rat dataset and called it CELdata.

CELdata
AffyBatch object
size of arrays=834x834 features (19 kb)
cdf=Rat230_2 (31099 affyids)
number of samples=8
number of genes=31099
annotation=rat2302
notes=

features=featureNames(CELdata)
>length(features)
[1] 31099
>sum(is.na(features))
[1] 0

I use features to query biomaRt for the Entrez-ids.  I got back only 18882 probesets (but actually fewer, because some probesets are matched to 2 Entrez-ids).  On the other hand, some of the Affy-ids there were returned did not match anything, so I am not sure why they were returned.

matchFeature=getBM(attributes=c('affy_rat230_2','entrezgene'), filters ='affy_rat230_2', values = features, mart = ensembl)
>dim(matchFeature)
[1] 18882     2
>sum(!is.na(matchFeature$affy_rat230_2))
[1] 18882
>sum(!is.na(matchFeature$entrezgene))
[1] 17814


I then use the non-missing Entrez-ids  to query biomaRt for the Affy-ids.  I got back only 18249 Entrez-ids (presumable because some Entrez-ids are matched to 2 probesets).  Nothing is missing.



matchEntrez=getBM(attributes=c('affy_rat230_2','entrezgene'), filters ='entrezgene', values = matchFeature[!is.na(matchFeature[,2]),2], mart = ensembl)

>dim(matchEntrez)
[1] 18249     2
>sum(!is.na(matchEntrez[,1]))
[1] 18249
>sum(!is.na(matchEntrez[,2]))
[1] 18249


  I am pretty sure that the discrepancies in the counts has to do with 
how getBM is handling multiple matches.

length(unique(matchFeature[,1]))
[1] 16851
>length(unique(matchEntrez[,1]))
[1] 16143
>length(unique(matchFeature[,2]))
[1] 13738
>length(unique(matchEntrez[,2]))
[1] 13737
>length(unique(matchFeature[!is.na(matchFeature[,2]),1]))
[1] 16142



In any case, I seem to be missing about 13000 probesets.  Surely there
cannot be that many probesets on the array with no Entrez-id?

Thanks for any help you can provide.

Naomi Altman


>sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages:
[1] rat2302cdf_2.13.0    hgu95av2cdf_2.13.0   AnnotationDbi_1.24.0 biomaRt_2.18.0
[5] edgeR_3.4.2          limma_3.18.13        affy_1.40.0          Biobase_2.22.0
[9] BiocGenerics_0.8.0

loaded via a namespace (and not attached):
  [1] affyio_1.30.0         BiocInstaller_1.12.0  DBI_0.2-7             IRanges_1.20.7
  [5] preprocessCore_1.24.0 RCurl_1.95-4.1        RSQLite_0.11.4        stats4_3.0.2
  [9] tools_3.0.2           XML_3.98-1.1          zlibbioc_1.8.0

   




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