 Dear List,

I used the following R code to extrace sequence information of a particular
probeset for PM probes of Affymetrix SNP6 array. However, for 100 probesets
I tested there were only 2 unique PM sequences for each probeset.  It
appears that the PM sequences were not correctly catalogued.

===============
library(pd.genomewidesnp.6)

db(pd.genomewidesnp.6)->kao

dbGetQuery(kao,"SELECT * from featureSet limit 100")$"man_fsetid"->probesets
result<-vector("list",length(probesets))
names(result)<-probesets

for(ind in 1:length(result)){

dbGetQuery(kao,paste("SELECT * from featureSet where
man_fsetid='",names(result)[ind],"'",sep=""))$fsetid->fsetid

dbGetQuery(kao, paste("select * from pmfeature where
fsetid=",fsetid,sep=""))->pm.100

c(pm.100$fid)->totiao
paste("fid=",paste(totiao,collapse=" or fid="),sep="")->totiao
paste("SELECT * from sequence where ",totiao,sep="")->totiao
dbGetQuery(kao,totiao)->seq

result[[ind]]<-seq

}


sapply(result, function(xxx) length(unique(xxx$seq)))

===================

sessionInfo()

R version 2.8.0 (2008-10-20)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

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

other attached packages:
[1] pd.genomewidesnp.6_0.4.2 oligoClasses_1.4.0
Biobase_2.2.1            RSQLite_0.7-1
[5] DBI_0.2-4
==============


LiGang

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