[BioC] Sequence data and filtering

hrishikesh deshmukh d_hrishikesh at yahoo.com
Tue Dec 28 21:41:22 CET 2004

Dear Bioconductorians,

My sincere apologies if this email is duplicated.I
have searched the mailing list and could not find a
way to solve my problem: Find out the probe intensity
(PM adn MM) for HG_U95Av2 which fall in (200 to 20000
units) range and extract their respective PM
sequences. I have been able to filter the probes but
how do i extract the sequence data?! I am including
the small script which i have written for filtering,
now how do i extract sequence information.

Thanks in advance.


Data <- ReadAffy()
pmi <- pm(Data)
mmi <- mm(Data)
pbn <- probeNames(Data)
rng.pmi <- apply(pmi,1,range)
rng.mmi <- apply(mmi,1,range)

out.of.boundspm <- ((rng.pmi[1,] >=200) & (rng.pmi[1,]
out.of.boundsmm <- ((rng.mmi[1,] >=200) & (rng.mmi[1,]

in.bounds <- (out.of.boundspm & out.of.boundsmm) 

ac1 <- 1:201800
ac2 <- ac1[in.bounds]

h.pbn <- pbn[ac2]
h.pmi <- pmi[ac2,]
h.mmi <- mmi[ac2,]

normal.data <- cbind(h.pbn,h.pmi,h.mmi)
names(normal.data) <-
write.table(normal.data, file="normaldata.txt",quote
=F,row.names=F,col.names=T,sep = " ")


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