Hi Michael,

The baseMean column is not on the log scale; it is the mean of normalized
counts for a gene. The intercept from the GLM is labelled intercept in
mcols(dse).

Mike
On Mar 28, 2013 5:00 PM, "Michael Muratet" <mmuratet@hudsonalpha.org> wrote:

> Greetings
>
> I have an experiment:
>
> > design(dse)
> ~ factor1 + factor2 + factor3
>
> where factor1 has two levels, factor2 has three levels and factor3 has
> three levels. I extract a gene of interest from the results for each term
> (I've changed the indices to reflect the condition):
>
> > lapply(resultsNames(dse),function(u) results(dse,u)["gene_A",])
> [["Intercept"]]
>         baseMean log2FoldChange        pvalue           FDR
> gene_A 1596.548       10.77485 3.309439e-216 7.025442e-216
> [["factor1_level2"]]
>         baseMean log2FoldChange    pvalue       FDR
> gene_A 1596.548      0.3386776 0.1307309 0.3587438
> [["factor2_level2"]]
>         baseMean log2FoldChange    pvalue       FDR
> gene_A 1596.548     -0.6882543 0.0613569 0.1007896
> [["factor2_level3"]]
>         baseMean log2FoldChange   pvalue       FDR
> gene_A 1596.548      0.2393368 0.513216 0.6589575
> [["factor3_level2"]]
>         baseMean log2FoldChange    pvalue       FDR
> gene_A 1596.548      0.1584153 0.6423634 0.8503163
> [["factor3_level3]]
>         baseMean log2FoldChange       pvalue         FDR
> gene_A 1596.548      -1.627898 1.823141e-06 0.001409384
>
> I want to be sure I understand the output format. Is it true that the
> coefficients (the vector beta) from the fit are the baseMean value scaled
> by the log2FoldChange? Is the true intercept value
> 1596.548*2^10.77485=2797274.13?
>
> mcols() tells me that the baseMean term is calculated over "all rows". The
> baseMean is different for different genes although it is the same for each
> gene across all the conditions, I'm not seeing how the rows are selected.
>
> Thanks
>
> Mike
>
> Michael Muratet, Ph.D.
> Senior Scientist
> HudsonAlpha Institute for Biotechnology
> mmuratet@hudsonalpha.org
> (256) 327-0473 (p)
> (256) 327-0966 (f)
>
> Room 4005
> 601 Genome Way
> Huntsville, Alabama 35806
>
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