[BioC] option rm.mask=TRUE in ReadAffy

[t-kawai at hhc.eisai.co.jp]

I have the same problem with expresso() as weiss.

To solve this problem, I executed a series of procedures step by step.

Background correction, I think, needs all of the CEL data wether those are
to be masked or not.  From the normalization step, I removed masking data
using Affy's original mask file.

For example,

## read CEL files
dat0 <- ReadAffy();

## Normalization step
dat <- bg.correct.mas(dat0);

## read mask file (in this case, 1803 probes to be masked)
msk <- scan("Hu6800_ClassA.MSK", skip=2, list("", ""));

## set ids (cell index list to be masked)
## (in this case, 59540 cells will be masked)
for (i in 1:length(msk[[1]])) {
        nam <- msk[[1]][i];
        txt <- gsub("-", ":", msk[[2]][i]);
        lst <- eval(parse(text=paste("c(", txt, ")")));

        if (i == 1) {
                ids <- pmindex(dat, nam)[[1]][lst];
        } else {
                ids <- c(ids, pmindex(dat, nam)[[1]][lst]);
        }
        ids <- c(ids, mmindex(dat, nam)[[1]][lst]);
}

## set NAs to cells to be maksed
intensity(dat)[ids, ] <- NA;

## Normalization step
dat1 <- normalize.AffyBatch.qspline(dat);

## Probe correction & summary step
dat2 <- computeExprSet(dat1, pmcorrect="mas", summary.method="liwong");
write.exprs(dat2, file="result.lst");



The file "Hu6800_ClassA.MSK" looks like
Hu6800
[Call]
A28102_at       17,18,19,20
AB000381_s_at   7
AC000064_cds2_at        18,19,20
...
M81830_at       1-20
M83181_at       1-20
...


Above script works rightly?  Please give me a comment...

Kawai

_______________________________________

Takatoshi Kawai, Ph.D.

Senior Sientist, Bioinformatics
Laboratoy of Seeds Finding Technology
Eisai Co., Ltd.
5-1-3 Tokodai, Tsukuba-shi,
Ibaraki 300-2635, Japan

TEL: +81-29-847-7192
FAX: +81-29-847-7614
e-mail: t-kawai at hhc.eisai.co.jp