[BioC] Missing columns in write.fit() and poorer precision than topTable()

James W. MacDonald jmacdon at med.umich.edu
Wed Mar 5 15:28:27 CET 2008

If you want the topTable output, why don't you just output that?

out <- topTable(fit2)
write.table(out, "fit2.xls", row.names=FALSE, sep="\t")



Ng Stanley wrote:
> Hi,
> Using the two functions:
> A) topTable(fit2, adjust.method="BH")
> B) write.fit(fit2, file="fit2.xls", adjust = "BH")
> How can I generate the logFC and adjusted.p.values as seen in topTable, for
> write.fit ?
> Also, how can I make the precision in write.fit the same as topTable ?
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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