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

Hi Brendan, maanova is not part of Bioconductor, so you are looking in the wrong place. If you want help with maanova, you should probably contact Hao Wu, who is the guy who wrote all the functions. hao@jax.org Alternatively, you might be able to find what you are looking for in the maanova user's manual. Jim James W. MacDonald UMCCC Microarray Core Facility 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> "Brendan Heavey" <bmheavey@buffalo.edu> 06/30/03 01:18PM >>> 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 _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor