[BioC] limma printer layout

[Gordon K Smyth]

Dear Jose,

My suggestion: don't remove the empty spots in the first place.

Best wishes
Gordon

> Date: Mon, 2 Mar 2009 09:48:48 -0600
> From: Jose Coria <com90185 at gmail.com>
> Subject: [BioC] limma printer layout
> To: bioconductor at stat.math.ethz.ch
>
> I'm trying to plot background intensity after clean empty values. When I
> check the information through layout, I got ngrid.r=12, ngrid.c=4,
> nspot.r=25, nspot.c=24 (28800 spots)
> Cleaning empty data I have 27003 spots., searching in forum I found this
> suggestion:
>
> Dear Vanessa,
>>
>> limma always assumes complete print-tip-groups, so the only way to
>> use imageplot() correctly is to complete your arrays by putting back
>>
>> to last 4 spots of each print-tip-group as NA. You can do this by:
>>
>>    narrays <- ncol(RG_e1)
>>    Y <- matrix(NA,21632,narrays)
>>    RG <- new("RGList",list(R=Y,G=Y,Rb=Y,Gb=Y)
>>    RG$printer <- RG_e1$printer
>>
>>    missingspots <- spotr(RG$printer)==26 & spotc(RG$printer)>=23
>>    RG$R[!i,] <- RG_e1$R
>>    RG$Rb[!i,] <- RG_e1$Rb
>>    RG$G[!i,] <- RG_e1$G
>>    RG$Gb[!i,] <- RG_e1$Gb
>>
>> Best wishes
>>
>> Gordon
>>
>> but If i try to follow the commands I have this error message:
>
> missingspots <- spotr(RG1$printer)==26 & spotc(RG1$printer)>=23
> Error en 1:layout$nspot.r : Argumento NA/NaN
> Can anyone suggest me something?
> Thanks
>
> -- 
> José Antonio Coria Fernández
> Universidad Nacional Autonóma de México
> Facultad de Estudios Superiores Acatlán
> Centro de Desarrollo Tecnológico
> (Departamento Servicios de Cómputo)
> Av. Alcanfores y San Juan Totoltepec S/N
> C.P. 53150  Tel: 56 23 17 62, 56 23 15 07
> Cubiculo 114 Planta Alta
> email: com90185 at gmail.com,
>         jcoriafdz at hotmail.com
>
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