Hee Siew Wan
g0203658 at nus.edu.sg
Sun Nov 7 08:25:00 CET 2004
I was trying to use a trial data (Dilution) to create a new cdf using "altcdfenvs". Instead of using "matchprobes", I created the "m":
ind <- c(seq(1,199084,by=11), seq(1,199084,by=10), seq(1,199084,by=9),
seq(1,199084,by=8), seq(1,199084,by=7), seq(1,199084,by=6))
m.dil <- new.env()
m.dil$match <- list(ind)
m.dil$match <- c(m.dil$match, ind[2:length(ind)])
m.dil <- as.list(m.dil)
length(m.dil$match) #  146637
id.dil <- hgu95av2probe$Probe.Set.Name[ind]
dil.cdf <- buildCdfEnv.matchprobes(m.dil, id.dil, nrow.chip=640, ncol.chip=640,
new.dil <- Dilution[,1:2]
validAffyBatch(new.dil, dil.cdf) #  TRUE
new.dil.cdfenv <- dil.cdf at envir <mailto:dil.cdf at envir>
new.dil at cdfName <mailto:new.dil at cdfName> <- "new.dil.cdfenv"
size of arrays=640x640 features (6405 kb)
cdf=new.dil.cdfenv (12453 affyids)
number of samples=2
number of genes=12453
As noted above, I have 12453 probe sets with my new cdf but I also have 12453 probe pairs when in fact I want 146637 probe pairs. The new cdf only returns 1 probe pair per set. Is there a way where I can have the 146637 probe pairs?
I tried doing the same thing for ath1121501 array. For this case, I created a data.frame from "ath1121501probe" with the following columns:
 "sequence" "probe" "X" "Y" "position"
However, when I run
m <- matchprobes(newath$sequence, ath1121501probe$sequence)
I found out that for some sequences, I have more than 1 match. For example,
Hence, the probe that I'm interested in may not be matched to the correct one.
The versions I'm using:
on Windows XP Professional Version 2002.
Did I do something wrong along the way for both methods? I'd appreciate any help or advice regarding how to get the selected probe pairs for analysis. Also, how do I cite the package "altcdfenvs"? Thank you.
Hee, Siew Wan
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