limma topTable values
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@john-seers-ifr-1605
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@sean-davis-490
Last seen 12 weeks ago
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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
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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 Norwich Research Park Colney Norwich NR4 7UA tel +44 (0)1603 251497 fax +44 (0)1603 507723 e-mail john.seers at bbsrc.ac.uk e-disclaimer at http://www.ifr.ac.uk/edisclaimer/ Web sites: www.ifr.ac.uk www.foodandhealthnetwork.com -----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
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