[BioC] How to include printtipweights and exclude control spots in single lmFit command

[Wolfgang Huber]

Dear Agnieszka

I have not tried this, but I think you want to do the 'isGene' 
subsetting synchronously with 'MAmu3A' and 'combwmu3', i.e.

fitmu3 <- lmFit(object = MAmu3A[isGene, ],
                 weights = combwmu3[isGene, ])

Btw, next time please provide a reproducible example, and the output of 
sessionInfo().

	Best wishes
	Wolfgang

  Zmienko wrote:
> 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]]
> 
> 
> 
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-- 

Best wishes
      Wolfgang

-------------------------------------------------------
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber