[BioC] limma and ArrayVision

Gordon Smyth smyth at wehi.edu.au
Sat Sep 27 17:29:41 MEST 2003

The below is now implemented in limma 1.2.5 which can be downloaded from 


>Thanks for the example ArrayVision file that you sent me. I now have two 
>examples of ArrayVision files from different people - I give the first 3 
>lines of the two files below. It is clear that the ArrayVision files are 
>designed for reading in to Excel but not for anything else. Note the 
>column-names over two lines and the use of non-ascii characters. (Question 
>marks "?" indicate that the character was not recognized by my text 
>editor.) In the first example there is no explicit information about which 
>columns were Cy3 and which were Cy5.
>This is what I propose to do for ArrayVision files.
>- I will assume that the leading columns (not counting the first column) 
>are Cy5 measurements and the trailing columns are Cy3.
>- I will assume that columns labeled something like "Median Dens - RFU / 
>µm2" are the foreground intensities and that those labeled "Bkgd" are the 
>Any other ideas?
>LINE 1: ,Ctrl,Ctrl,Ctrl,Ctrl,Data,Data,Data,Data,
>LINE 2: Spot labels,Median Dens - RFU / µm2,MAD - RFU / 
>µm2,Bkgd,sMedianDens,Median Dens - RFU / µm2,MAD - RFU / µm2,Bkgd,sMedianDens,
>LINE 3: R1 - C1 : 1,29.072,11.878,33.825,0.000,1.247,0.299,0.642,0.605,
>LINE 1: ,"Cy5 right","Cy5 right","Cy5 right","Cy5 right","Cy5 right","Cy3 
>right","Cy3 right","Cy3 right","Cy3 right","Cy3 right"
>LINE 2: "Spot labels","Median Dens - RFU / ?m2","SD - RFU / ?m2","Area - 
>?m2","Bkgd","nMedianDens","Median Dens - RFU / ?m2","SD - RFU / ?m2","Area 
>- ?m2","Bkgd","nMedianDens"
>LINE 3: "B1 : R1 - C1",0.298,0.161,38400,0.303,0,0.499,0.171,38400,0.492,0.002

At 09:15 PM 26/09/2003, alessandro ambrosi wrote:
>Hi all,
>first of all thanks again for all your help.
>Reading ArrayVision files sometimes I get the following
>> > read.maimages("2706L.csv", source="arrayvision", sep=",")
>>Error in "[.data.frame"(obj, , columns$Gb) :
>>         not all specified columns exist
>I noted that ArrayVision files have not a standard number of
>columns and it depends on which informations user decided to
>save. So the interesting columns (relative to intensity and
>background) can change position. One must pay attention that
>Ctrl Median Dens -> Rf = 2,
>Ctrl Bkg         -> Rb = 5,
>Data Median Dens -> Gf = 7,
>Data Bkg         -> Gb = 10
>Hope it helps.
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

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