Entering edit mode
Dear All,
I am using Affymetrix Mouse Gene ST 2.0 arrays and after normalization wanted to annotate my ExpressionSet. I loaded the required library as
> library("mogene20sttranscriptcluster.db")
Loading required package: org.Mm.eg.db
Warning message:
In rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
which gave a warning. Next I saved the annotation as :
> Annot <- data.frame(ACCNUM=sapply(contents(mogene20sttranscriptclusterACCNUM), paste, collapse=", "), SYMBOL=sapply(contents(mogene20sttranscriptclusterSYMBOL), paste, collapse=", "), DESC=sapply(contents(mogene20sttranscriptclusterGENENAME), paste, collapse=", "))
but it returned all probes as NA
> head(Annot)
ACCNUM SYMBOL DESC
17200001 NA NA NA
17200003 NA NA NA
17200005 NA NA NA
17200007 NA NA NA
17200009 NA NA NA
17200011 NA NA NA
Any hint what is going wrong ??
Here is the Sessioninfo:
R version 3.4.0 (2017-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.5 LTS Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.0 LAPACK: /usr/lib/lapack/liblapack.so.3.0 locale: [1] LC_CTYPE=en_IN.UTF-8 LC_NUMERIC=C LC_TIME=en_IN.UTF-8 LC_COLLATE=en_IN.UTF-8 [5] LC_MONETARY=en_IN.UTF-8 LC_MESSAGES=en_IN.UTF-8 LC_PAPER=en_IN.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] mogene20sttranscriptcluster.db_8.4.0 org.Mm.eg.db_3.4.1 pd.mogene.2.0.st_3.14.1 [4] DBI_0.7 RSQLite_2.0 genefilter_1.54.2 [7] annotate_1.50.1 XML_3.98-1.9 AnnotationDbi_1.38.1 [10] limma_3.28.21 oligo_1.36.1 Biostrings_2.40.2 [13] XVector_0.12.1 IRanges_2.6.1 S4Vectors_0.10.3 [16] oligoClasses_1.34.0 affy_1.50.0 Biobase_2.32.0 [19] BiocGenerics_0.18.0 loaded via a namespace (and not attached): [1] Rcpp_0.12.12 BiocInstaller_1.22.3 compiler_3.4.0 GenomeInfoDb_1.8.7 [5] bitops_1.0-6 iterators_1.0.8 tools_3.4.0 zlibbioc_1.18.0 [9] digest_0.6.12 bit_1.1-12 lattice_0.20-35 memoise_1.1.0 [13] preprocessCore_1.34.0 tibble_1.3.3 ff_2.2-13 pkgconfig_2.0.1 [17] rlang_0.1.1 Matrix_1.2-10 foreach_1.4.3 affxparser_1.44.0 [21] grid_3.4.0 bit64_0.9-7 survival_2.41-3 blob_1.1.0 [25] codetools_0.2-15 GenomicRanges_1.24.3 splines_3.4.0 SummarizedExperiment_1.2.3 [29] xtable_1.8-2 RCurl_1.95-4.8 affyio_1.42.0
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As I already noted in my answer, not all of the probes on the array measure a 'gene'! You are looking at the first few probesets on the array, which are intronic controls, and are then saying that the package doesn't work. If you ask 'what gene does this thing measure?' and it's an intronic control, the answer is 'It doesn't measure a gene, it's an intronic control'. I can't make it any clearer than that.
> z <- select(hugene20sttranscriptcluster.db, keys(hugene20sttranscriptcluster.db), c("SYMBOL","ENTREZID")) 'select()' returned 1:many mapping between keys and columns > apply(z, 2, function(x) sum(is.na(x))) PROBEID SYMBOL ENTREZID 0 21563 21563 > dim(z) [1] 59281 3 > head(z) PROBEID SYMBOL ENTREZID 1 16650001 <NA> <NA> 2 16650003 <NA> <NA> 3 16650005 <NA> <NA> 4 16650007 <NA> <NA> 5 16650009 <NA> <NA> 6 16650011 <NA> <NA> > z[5000:5010,] PROBEID SYMBOL ENTREZID 5000 16670270 PPIAL4E 730262 5001 16670270 PPIAL4D 645142 5002 16670270 PPIAL4F 728945 5003 16670270 PPIAL4C 653598 5004 16670270 PPIAL4A 653505 5005 16670270 PPIAL4G 644591 5006 16670270 LOC105371242 105371242 5007 16670272 LOC105371196 105371196 5008 16670272 LOC105371214 105371214 5009 16670276 LOC645166 645166 5010 16670276 LOC100996732 100996732 >