Hi, everyone, I want to use FIRMAGene to analysis differencial splicing of
hugene-1.0-st array ,there is no overlap between Ensembl identifiers from
getUnitNames() and Affymetrix identifiers in 'hgnetaffx'.follows my code:
>library(aroma.affymetrix)
>library(FIRMAGene)
>hgnetaffx <-
read.csv("HuGene-1_0-st-v1.na25.hg18.transcript.csv",sep=",",skip=19,header=TRUE,comment.char="",stringsAsFactors=FALSE)
cdf <- AffymetrixCdfFile$byChipType('HuGene-1_0-st-v1', tags="Ensembl,exon")
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/HuGene-1_0-st-v1
Filename: HuGene-1_0-st-v1,Ensembl,exon.cdf
File size: 28.51 MB (29891482 bytes)
Chip type: HuGene-1_0-st-v1,Ensembl,exon
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 1050x1050
Number of cells: 1102500
Number of units: 27901
Cells per unit: 39.51
Number of QC units: 0
> u <- which(getUnitNames(cdf) %in% hgnetaffx$probeset_id[hgnetaffx$category
> == "main" & hgnetaffx$total_probes > 7 & hgnetaffx$total_probes < 200])
> u[1:200]
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[42] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[83] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[124] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[165] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
NA NA NA NA NA NA NA NA NA NA NA NA NA
> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: i386-w64-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=Chinese_People's Republic of China.936
LC_CTYPE=Chinese_People's Republic of China.936
[3] LC_MONETARY=Chinese_People's Republic of China.936 LC_NUMERIC=C
[5] LC_TIME=Chinese_People's Republic of China.936
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] aroma.affymetrix_2.7.0 affxparser_1.28.1 aroma.apd_0.2.3
R.huge_0.4.1 aroma.light_1.28.0
[6] aroma.core_2.7.0 matrixStats_0.6.2 R.rsp_0.8.2
R.devices_2.1.3 R.cache_0.6.5
[11] R.filesets_1.6.0 digest_0.6.0 R.utils_1.18.0
R.oo_1.10.2 FIRMAGene_0.9.7
[16] R.methodsS3_1.4.2
loaded via a namespace (and not attached):
[1] PSCBS_0.30.0
how can i fix it? did i download the wrong version of annotation?I download
the HuGene-1_0-st-v1.na25.hg18.transcript.csv from www.affymetix.com ;and
HuGene-1_0-st-v1.probe.tab from
http://media.affymetrix.com/analysis/downloads/na23/wtgene/HuGene-1_0-st-v1.probe.tab.zip
i can not find probe.tab of na25.
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