[BioC] limma topTable columns and new interface?

[Sean Davis]

On Thu, Apr 15, 2010 at 5:17 AM, Timothy Wu <2huggie at gmail.com> wrote:
> Hi,

Hi, Timothy.

> In Limma I run topTable for Affy chips. After write.table(), there are 8
> columns of data, but only 7 headers (and they are misplaced to the left by 1
> position). The last column "B" is log odd, correct? What is the data in the
> first column?

These are the row names in the first column.  See the help for write.table().

> Also, the topTable help says "toptable is an earlier interface and is
> retained only for backward compatibility." So is it deprecated? What is the
> new interface?

toptable and topTable() are two different functions.  I believe the
latter version is preferred over the former.

Hope that helps.

Sean