[BioC] Labels in exprs to plot

[James MacDonald]

The easiest way I know to do this is to use list.celfiles() when you
read in your AffyBatch.

abatch <- read.affybatch(filenames=list.celfiles())

If you simply use ReadAffy(), you will get the entire path and will have
to use sub() to truncate later.

HTH,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
>>> <mcolosim at brandeis.edu> 08/14/04 10:11 AM >>>
Hi,

I'm having the hardest time trying to get the correct labels from my
exprs to
plot correctly. I'm using the affy to read in cels and process them.
However,
the lables I get are the "fullpath" to the files and not the ones in
pData.

Is there a way to get the correct labels minus the .CEL from pData to be
used
as labels for plot (even exprs2excel is now printing out the full paths,
which it didn't do before).

Basically I clustered my arrays and want to view it, but with the full
path as
labels it is tiny.

hcRMA <- hclust(....)
plot(hcRMA, labels = ?, main = "Hierarchical clustering dendrogram"

Thanks
Marc

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