Hi!
I am trying to analyze two-colour cDNA arrays, 
with the simplest possible design, four 
replicates, no dye-swaps, treatment =Cy5, ctrl=Cy3.

I used printtipWeights function on my normalized data

 >printtipw=printtipWeights(MAmu3A)

Then I used asMatrixWeights function and 
multiplied printTipWeights and printtipweights

 >2mu3<-asMatrixWeights(printtipw,c(31200,4))
 >combwmu3<-w2mu3*MAmu3A$weights

At least that's what I wanted to...

Then, according to limma guide examples, I wanted 
to exclude control and empty spots from my 
analysis, so I used spottype Status, previously assigned

 >isGene<-MAmu3A$genes$Status == "cDNA"


But I can not put it in one lmFit command with the combined weights:

 > fitmu3<-lmFit(MAmu3A[isGene, ], weights=combwmu3)
Error in asMatrixWeights(weights, dim(M)) :
   weights is of unexpected shape

However, I can use lmFit function without 
combwmu3, or with combwmu3, but not excluding control and empty spots:

 > fitmu3<-lmFit(MAmu3A[isGene, ])
or
 > fitmu3comb<-lmFit(MAmu3A, weights=combwmu3)

please help me deal with it, cause I am not 
creative when considering R enviroment....

Many thanks

Agnieszka



Dr Agnieszka ¯mieñko

Centrum Doskonalosci CENAT
Instytut Chemii Bioorganicznej Polskiej Akademii Nauk
Noskowskiego 12/14
61-704 Poznañ
tel. (61) 8528503 wew. 249
fax: (61) 8520532

Agnieszka Zmienko, Ph.D.

CENAT
Institute of Bioorganic Chemistry
Polish Academy of Sciences
Noskowskiego 12/14
61-704 Poznan, Poland
phone (0048) 61-8528503 ext. 249
fax: (0048) 61-8520532 
	[[alternative HTML version deleted]]

