[BioC] Doubt and Problem(?) with analysis with marray tools

[Marcelo Luiz de Laia]

I followed all of the steps to make a normalization using the tool
marrayNorm.
I normalized the data and I saw the plotgraphs. All is good.
However, I have a doubt and a problem.

Doubt:
My genes are spoteds two times in the membrane (in duplicate). I generated
the file of data with all of the duplicated genes, 7680 spots.
When I executed the command maM(ka.susc.norm), I could verify that the genes
continued duplicated. I ask: Should I must get the average among the two
genes (duplicates) before normalizing them? Or does the tool marray detect
the duplicity of the genes and does it already execute the average between
both and, in this case, did I execute some wrong step during the process?

Problem:
In my membrane exist 530 empty spots (without DNA). When I accomplish the
normalization, these spots receive the value "NA". That is a problem?

Today, in the morning, I tried to transform my object marrayNorm
(ka.susc.norm) in an object limma using the function "as.MAList."
The error

> MA <- as.MAList(ka.susc.norm)
Error in if (length(x) && x != "") return(x) else return(NULL) :
        missing value where TRUE/FALSE needed

occurred which I believe to be due to these "NA" in all of the slides. I see
the help for as.MAList (?as.MAList) previous, but I do not solve the
problem.

How could I solve this problem and to cure this doubt?

Thanks for any comments

Marcelo Luiz de Laia, M.Sc.
Dep. de Tecnologia, Lab. Bioquímica e de Biologia Molecular
Universidade Estadual Paulista - UNESP
Via de Acesso Prof. Paulo Donato Castelane, Km 05
14.884-900 - Jaboticabal, SP, Brazil
PhoneFax: 16 3209-2675/2676/2677 R. 202/208/203 (trab.)
Phone res: 16 3203 2328 - www.lbm.fcav.unesp.br - mlaia at yahoo.com
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