Dear List,



Normally I use the batch query mode of the NetAffx (affymetrix website) to annotate my gene lists (downside: It can do only 10K probes at a time).

I decided to try the R packages to do the same.



However, I decided to check a couple of probes to see if the output in either case is the same but it is not! So I do not know where the error lies: in my code, in the meta data packages or the website or if I have the incorrect array package?





> eset

ExpressionSet (storageMode: lockedEnvironment)

assayData: 32321 features, 21 samples

  element names: exprs, se.exprs

protocolData

  sampleNames: CD8 5_14_(HuGene-1_0-st-v1).CEL CD8

    5_16_(HuGene-1_0-st-v1).CEL ... CD8 6_8_(HuGene-1_0-st-v1).CEL (21

   total)

  varLabels: ScanDate

  varMetadata: labelDescription

phenoData

  sampleNames: CD8 5_14_(HuGene-1_0-st-v1).CEL CD8

    5_16_(HuGene-1_0-st-v1).CEL ... CD8 6_8_(HuGene-1_0-st-v1).CEL (21

    total)

  varLabels: sample

  varMetadata: labelDescription

featureData: none

experimentData: use 'experimentData(object)'

Annotation: hugene10stv1



> library(annotate)

> library(hugene10stv1cdf)

> library(hugene10sttranscriptcluster.db)

> ls("package:hugene10sttranscriptcluster.db")

> ID <- featureNames(eset)

> Symbol <- getSYMBOL(ID, "hugene10sttranscriptcluster.db")

> Name <- as.character(lookUp(ID, "hugene10sttranscriptcluster.db", "GENENAME"))

> Entrez <- as.character(lookUp(ID, "hugene10sttranscriptcluster.db", "ENTREZID"))



> tail(Symbol)

     8180413      8180414      8180415      8180416      8180417      8180418

"ST6GALNAC4" "ST6GALNAC1"     "MCART1"      "OR3A2"    "METTL2B"           NA



> tail(ID)

[1] "8180413" "8180414" "8180415" "8180416" "8180417" "8180418"



> tail(Entrez)

[1] "27090" "55808" "92014" "4995"  "55798" "NA"





Which does not match the output from the website below for the same set of IDs:

*         GeneChip(r) Human Gene 1.0 ST Array

Displaying Results: 1-6 of 6.



Transcript Cluster ID

GO Description

Chromosome

Gene Title

Pathway

Gene Symbol

Entrez Gene ID

Cytoband


8180416















8180417















8180418















8180413















8180414















8180415


















> sessionInfo()

R version 2.15.0 (2012-03-30)

Platform: x86_64-pc-linux-gnu (64-bit)



locale:

[1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C

 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8

 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8

 [7] LC_PAPER=C                 LC_NAME=C

 [9] LC_ADDRESS=C               LC_TELEPHONE=C

[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C



attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base



other attached packages:

[1] hugene10sttranscriptcluster.db_8.0.1 hugene10stprobeset.db_8.0.1

 [3] org.Hs.eg.db_2.7.1                   RSQLite_0.11.1

 [5] DBI_0.2-5                            annotate_1.34.0

 [7] rgl_0.92.892                         R.utils_1.12.1

 [9] R.oo_1.9.3                           R.methodsS3_1.2.2

[11] plotrix_3.4                          hugene10stv1cdf_2.10.0

[13] AnnotationDbi_1.18.0                 scatterplot3d_0.3-33

[15] WriteXLS_2.1.0                       affyQCReport_1.34.0

[17] lattice_0.20-6                       affy_1.34.0

[19] Biobase_2.16.0                       BiocGenerics_0.2.0

[21] gdata_2.8.2                          limma_3.12.0



loaded via a namespace (and not attached):

[1] affyio_1.24.0         affyPLM_1.32.0        BiocInstaller_1.4.7

 [4] Biostrings_2.24.1     gcrma_2.28.0          genefilter_1.38.0

 [7] grid_2.15.0           gtools_2.6.2          IRanges_1.14.2

[10] preprocessCore_1.18.0 RColorBrewer_1.0-5    simpleaffy_2.32.0

[13] splines_2.15.0        stats4_2.15.0         survival_2.36-14

[16] tcltk_2.15.0          tools_2.15.0          xtable_1.7-0

[19] zlibbioc_1.2.0





Any help/suggestion would be appreciated.

Apologies if this is posted more than once!!





Many Thanks,

Natasha





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