[BioC] maanova rss for null model
Brendan Heavey
bmheavey at buffalo.edu
Mon Jun 30 14:18:26 MEST 2003
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
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