[BioC] limma printer layout

[Gordon K Smyth]

Dear Maciej,

In my posting of 9 September 2007, the variable "missingspots" should be 
"i".  (I shortened it to make the following four lines of code easier to 
read.)  There is also a missing parentheses.  The code should have been:

    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
    i <- 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: Sun, 30 Oct 2011 01:23:35 +0200
> From: mjonczyk <mjonczyk at biol.uw.edu.pl>
> To: <bioconductor at r-project.org>
> Subject: Re: [BioC] limma printer layout
> Message-ID: <1f6831a24a2a202334f96e1c131c3a28 at biol.uw.edu.pl>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> 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$printer)>=17
>
> to set as NA every spot in row 17 to 22 in blocks 33 (9th grid row)
>  to 48
> Unfortunately it doesn't work.
>
> I also don't know how "missingvalues" object is utilized here.
>
> Thanks in advance,
> Maciej Jo?czyk
>
>
>> Dear Vanessa,
>>
>> limma always assumes complete print-tip-groups, so the only way to
>> use imageplot() correctly is to complete your arrays by putting back
>> to last 4 spots of each print-tip-group as NA. You can do this by:
>>
>>    narrays <- ncol(RG_e1)
>>    Y <- matrix(NA,21632,narrays)
>>    RG <- new("RGList",list(R=Y,G=Y,Rb=Y,Gb=Y)
>>    RG$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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