On Monday 02 April 2007 07:38, john seers (IFR) wrote:
> Dear Bioconductor users
>
> I am using limma to analyse some Affymetrix arrays. (First time I
have
> analysed Affymetrix ...)
>
> When I use "topTable" it returns a format that I have not seen
before.
> If I enter "?topTable" the help text does not describe this format
in
> the "Values" section. I have looked in the user manual but I cannot
find
> any information and I have generally searched but I cannot find a
> description of this format of topTable. Particularly I would like to
> know what AveExpr is and how it is calculated. I can guess what
logFC is
> but I would still like to see it documented somewhere.
An update to a newer version of limma will fix the issue. From
version
2.9.16:
Value:
A dataframe with a row for the 'number' top genes and the
following columns:
genelist: if genelist was included as input
logFC: estimate of the log2-fold-change corresponding to the effect
or contrast
AveExpr: average log2-expression for the probe over all arrays and
channels, same as 'Amean' in the 'MarrayLM' object
t: moderated t-statistic
P.Value: raw p-value
adj.P.Value: adjusted p-value or q-value
B: log odds that the gene is differentially expressed
Sean
Thanks Sean. That has fixed it.
I thought I was up to date with limma but a new version has crept in
when I wasn't looking.
John Seers
---
John Seers
Institute of Food Research
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Colney
Norwich
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e-mail john.seers at bbsrc.ac.uk
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Web sites:
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-----Original Message-----
From: Sean Davis [mailto:sdavis2@mail.nih.gov]
Sent: 02 April 2007 13:03
To: bioconductor at stat.math.ethz.ch
Cc: john seers (IFR)
Subject: Re: [BioC] limma topTable values
On Monday 02 April 2007 07:38, john seers (IFR) wrote:
> Dear Bioconductor users
>
> I am using limma to analyse some Affymetrix arrays. (First time I
have
> analysed Affymetrix ...)
>
> When I use "topTable" it returns a format that I have not seen
before.
> If I enter "?topTable" the help text does not describe this format
in
> the "Values" section. I have looked in the user manual but I cannot
find
> any information and I have generally searched but I cannot find a
> description of this format of topTable. Particularly I would like to
> know what AveExpr is and how it is calculated. I can guess what
logFC
is
> but I would still like to see it documented somewhere.
An update to a newer version of limma will fix the issue. From
version
2.9.16:
Value:
A dataframe with a row for the 'number' top genes and the
following columns:
genelist: if genelist was included as input
logFC: estimate of the log2-fold-change corresponding to the effect
or contrast
AveExpr: average log2-expression for the probe over all arrays and
channels, same as 'Amean' in the 'MarrayLM' object
t: moderated t-statistic
P.Value: raw p-value
adj.P.Value: adjusted p-value or q-value
B: log odds that the gene is differentially expressed
Sean
