[BioC] limma printer layout

[mjonczyk]

Dear All,

I have similar problem: my layout is
> RG$printer
$ngrid.r
[1] 12

$ngrid.c
[1] 4

$nspot.r
[1] 22

$nspot.c
[1] 22

but 16 last blocks, i.e. 33 and higher has only 16 rows.

So I tried to adapt the code, I set
missingspots=gridr(RG$printer)>=9 & spotr(RG$printer)>=17

to set as NA every spot in row 17 to 22 in blocks 33 (9th grid row)
  to 48
Unfortunately it doesn't work.

I also don't know how "missingvalues" object is utilized here.

Thanks in advance,
Maciej Jończyk


> 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
>
>>Date: Fri, 07 Sep 2007 14:12:45 +0200
>>From: Vanessa Vermeirssen <vanessa.vermeirssen at ...>
>>Subject: [BioC] limma printer layout
>>To: bioconductor at ...
>>Message-ID: <46E1403D.6090805 at ...>
>>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>>Hi,
>>
>>I am trying to read in cDNA spotted microarray data into limma.
>>I would like to check for spatial heterogeneity in the samples and
>>therefore I would like to define the printer layout.
>>
>>I have done this now using a dataframe containing the gene list and
>>columns for block, row and column of the array.
>>Through getLayout, I get correctly the 4 by 8,26 by 26 dimensions 
>> (21632
>>spots). However I noticed from the raw data that
>>in every block at row 26, 4 columns are skipped, so 4 spots are 
>> skipped.
>>Therefore in my datafile I only have 21504 spots.
>>When I try to check for spatial heterogeneity by:
>>  > imageplot(log2(RG_e1a$Gb[,1]),RG_e1a$printer)
>>Error in imageplot(log2(RG_e1a$Gb[, 1]), RG_e1a$printer) :
>>         Number of image spots does not agree with layout dimensions
>>I get this error...
>>
>>Is there a way to more precisely define my printer-layout or a way to
>>get around this and look at spatial heterogeneity anyway?
>>
>>I now copy my code completely, so you have an idea of what I have 
>> read
>>in already.
>>#reading cDNA spotted arrays in Limma Bioconductor package
>>library(limma)
>>targets_e1a <- readTargets()
>>RG_e1a <-read.maimages(targets_e1a$FileName,
>>columns=list(R="CH2I_MEDIAN",
>>G="CH1I_MEDIAN",Rb="CH2B_MEDIAN",Gb="CH1B_MEDIAN"),
>>annotation=c("NAME","Orfname","SECTOR","SECTORROW","SECTORCOL"))
>>names(RG_e1a$genes) <- c("ID", "Orfname", "Block", "Row", "Column")
>>RG_e1a$printer <- getLayout(RG_e1a$genes, guessdups=TRUE)
>>
>>
>>Thank you so much already,
>>Vanessa

-- 
Maciej Jonczyk,
Department of Plant Molecular Ecophysiology
Faculty of Biology, University of Warsaw
02-096 Warsaw, Miecznikowa 1
Poland



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