---------- Forwarded message ----------
From: Timothy Wu <2huggie@gmail.com>
Date: Thu, Apr 15, 2010 at 5:45 AM
Subject: Re: [BioC] limma topTable columns and new interface?
To: Sean Davis <seandavi@gmail.com>
Cc: bioconductor@stat.math.ethz.ch


Hi Sean,

Thanks for the quick reply.

On Thu, Apr 15, 2010 at 5:30 PM, Sean Davis <seandavi@gmail.com> wrote:
>
> On Thu, Apr 15, 2010 at 5:17 AM, Timothy Wu <2huggie@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().


> topTable(fit2, adjust.method="BH", number=10)

>                ID     logFC   AveExpr         t      P.Value
> adj.P.Val        B
> 12861   203413_at -4.863939  9.063835 -17.02642 5.096458e-16 2.786489e-11
> 25.33969
> 16463 207016_s_at -8.002118  7.819954 -15.55356 4.768779e-15 1.303665e-10
> 23.44225
> 10459 201010_s_at -4.086280 10.489258 -14.17960 4.503602e-14 8.207815e-10
> 21.48528
> 34429   225171_at -3.855857 10.257294 -13.88007 7.514060e-14 1.027078e-09
> 21.03252
> 15016   205568_at -4.293815  7.765863 -12.14548 1.733606e-12 1.648261e-08
> 18.20875
> 14531   205083_at -4.907075  7.403553 -12.12315 1.808792e-12 1.648261e-08
> 18.17003
> 51083   241833_at -6.651936  5.153752 -11.57349 5.234556e-12 4.088562e-08
> 17.19685
> 32874   223597_at -7.323707  8.198642 -11.33152 8.448496e-12 5.774019e-08
> 16.75594
> 14094   204646_at -3.634998  9.030261 -11.03786 1.524340e-11 9.260368e-08
> 16.21036
> 11291 201842_s_at -4.967125  9.415506 -10.94798 1.829875e-11 1.000484e-07
> 16.04104
>
> This is after topTable and before write.table(), I don't know what the
> first column means. I checked the Limma vignette, it doesn't seem to say.
> The topTable() help says there are, geneList, logFC, avgExpr, t, F (omitted
> unless more than one coef is specified), P.Value, adj.P.Value, and B. I
> don't see the column label for the first column.
>

The first "column" is not a column.  It contain row names.  They are not
part of the data but are only labels for the rows.

Sean


>
> > 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.
>

Oh! I see. :)

Timothy

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