[BioC] Help on basic skills on R and maanova

[Marcelo Laia]

Hi,

A nice weekend for you!

I was googled and found a script for extract the gene lists from a
volcano object.

Here is it:

output_mix.Trat<-cbind(
    idx.mix.Trat$idx.all,
    as.vector(ZA$CloneID[idx.mix.Trat$idx.all]),
    round(test.full.Trat.mix$obsAnova$Trat[idx.mix.Trat$idx.all],4),
    round(test.full.Trat.mix$F1$Pvalperm[idx.mix.Trat$idx.all,],4),
    round(test.full.Trat.mix$F3$Pvalperm[idx.mix.Trat$idx.all,],4),
    round(test.full.Trat.mix$Fs$Pvalperm[idx.mix.Trat$idx.all,],4),
    round(2^(test.full.Trat.mix$obsAnova$Trat[idx.mix.Trat$idx.all]-test.full.Trat.mix$obsAnova$Trat[idx.mix.Trat$idx.all+18855]),4))

write.table(output_mix.Trat,"output_mix.Trat.txt",sep="\t",dec=".")

It works fine!! :)

But, the header of out put file doesn't is user friendly.

It is like this:

V1	V2	V3	V4	V5	V6	V7	
1	160	LR1011G09	-0.0107	0.04	0.0539	0.0411	NA
2	187	LR1013F04	-0.4172	0.0325	0.0522	0.0353	NA
3	244	LR1017B12	-0.2078	0.0362	0.0405	0.0343	NA
4	355	LR1024D07	0.0283	0.0073	0.0344	0.0114	NA
5	512	LR1033B05	-0.2379	0.0409	0.0543	0.0418	NA

Here is my doubt: what means each one of these columns?

1s is the order of genes;
2s is the number of the gene in the original file (ZA)
3s is the name of the genes
from 4th to 8th I am not sure what it means!

There is a way to include the column header in the above script?

Plus, the script plus 18855 at the last line. Have you an ideia about
this number?

Your help is very appreciated. If you have another comments, they will
very welcome, too.

Thank you very much.

Best wishes

-- 
Marcelo Luiz de Laia