[BioC] Question about topTableF

[James W. MacDonald]

Hi Jose,

José Manuel Otero wrote:
> I am using the topTableF to view the outputs of my ANOVA on microarray data where I have 4 data sets:
> 
> wild-type/conditionA
> wild-type/conditionB
> mutant/conditionA
> mutant/conditionB
> 
> I am able to generate the appropriate contrasts matrix; and believe I am getting the right output.  However, I do not understand what the output is of the topTableF command.  If I use the normal topTable, where I specify a coefficient, then I see the typical column headers: B, adj P-value, P-value, etc.  But, when I look at all the coefficients, I see the F-statistic, P-value, and adjust P-value, and then under each comparison I make there is a number.  What is this statistic?
> 
> I hope I am being clear, and would appreciate any help.  Keep in mind, I am new to R and Limma, so please be specific.

Does running

example(lmFit)
topTable(fit)

help answer your question?

Best,

Jim


> 
> Thank you,
> Manny Otero
> 
> 
> Jose Manuel Otero
> PhD Student, BioCentrum-DTU
> 
> Center for Microbial Biotechnology
> Technical University of Denmark
> DTU Building 223
> Room 213
> 
> OFFICE TEL: +45 45 25 27 15
> MOBILE TEL: +45 28 40 45 25
> FAX: +45 45 88 41 48
> 
> jomo at biocentrum.dtu.dk
> 
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-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
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