[BioC] maanova rss for null model

[Brendan Heavey]

Hello-

I'm trying to recreate the calculation maanova goes through on my data.  In
the paper, it shows

    (rss0-rss1)/(df0-df1)]
F1= ----------------------
          (rss1/df1)

I have 6 biological replicates for each gene, and they're all spotted 3
times on each slide, and there is a dye flip (Design:
SampleID-1221-1221-1221-1221-1221-1221)

Maanova calculates a F1 score for each gene in the data.  I believe I know
how to calculate rss1 and df1 for each gene by the following:

1). Calculate Overall Mean for that gene
2). Subtract signal value from each spot signal across all 3 animals from #1
3). Square #2
4). Sum #3

I'm running into trouble trying to understand how to calculate rss0.  I
guess I'm confused about what the null model really represents...I thought I
would just find the overall mean from all spots/animals, subtract each
signal from that mean then sum the squares.  This doesn't appear to be
working.

Thanks ahead of time for any help you can provide...i greatly appreciate it