[BioC] Time course cDNA two color array analysis

[Marcelo Laia]

Dear Ana,

I try to use replicate spot and I get trouble in set up the index, the
match and matchID.col parameters.

I do this code:

> MA.2 <- normalizeWithinArrays(RG,method="printtiploess")
> IDs <- MA.2$genes$names # match vector
> indeX <- paste("g", rep(c(1:32), 216), sep = "")  # index vector
> masigproResult <- maSigPro(masigproData, add.IDs = FALSE,
+ IDs = NULL,  matchID.col = 1, trat.repl.spots = "average", index = indeX,
+ match = IDs, rs = 0, design, vars = "groups", min.obs = 3)

When I run this code, I get this error:

[1] "running design"
[1] "running p.vector"
[1] "fitting gene 100 out of 5173"
(...)
[1] "running T.fit"
[1] "fitting gene 100 out of 282"
[1] "fitting gene 200 out of 282"
[1] "running get.siggenes"
Error in prom[i, ] <- c : subscript out of bounds
In addition: There were 26 warnings (use warnings() to see them)

I read the help pages for average.rows, get.siggenes e maSigPro and
try the examples, but I don't understand how make these ones.

I did a analysis without consider replicates, and it looks very good!
I would like to compare the two results and get a little bit more
knowledge.

Thank you

-- 
Marcelo Luiz de Laia
Ph.D Candidate
São Paulo State University (http://www.unesp.br/eng/)
School of Agricultural and Veterinary Sciences
Department of  Technology
Via de Acesso Prof. Paulo Donato Castellane s/n
14884-900   Jaboticabal - SP - Brazil
Phone: +55-016-3209-2675
Cell: +55-016-97098526