Hi all! I tried to use read.maimages to read ArrayVision files as Gordon suggested. Unfortunately I get the following: > read.maimages("12371987B.csv", source="arrayvision", sep=",") Error in match.arg(source, c("spot", "spot.close.open", "genepix", "quantarray")) : ARG should be one of spot, spot.close.open, genepix, quantarray > I've just updated all the packages so I think this is not the problem. Have you any suggestion? Thank you a lot in advance, best Alessandro At 23.43 28/08/03 +1000, you wrote: >Thanks to help from Isaac Mehl, limma now supports ArrayVision data. The >support is in limma 1.1.12. > >The data file attached by Isaac is read by > > read.maimages("12371987B.csv", source="arrayvision", sep=",") > >Cheers >Gordon > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

> Hi all! > > I tried to use read.maimages to read ArrayVision files as Gordon > suggested. Unfortunately I get the following: > > > read.maimages("12371987B.csv", source="arrayvision", sep=",") > Error in match.arg(source, c("spot", "spot.close.open", "genepix", > "quantarray")) : > ARG should be one of spot, spot.close.open, genepix, quantarray > > > > I've just updated all the packages so I think this is not the problem. Yes it is the problem. The message that you quote is from limma version 1.0.8, i.e., the last official BioC release, rather than from limma 1.2.4 which is the most recent development version. You have apparently "updated all the packages" simply by re-installing the last official release of the packages. If you want newer versions of the packages, you have to install the development versions of the packages. Gordon > Have you any suggestion? > > Thank you a lot in advance, > best > Alessandro > > > > At 23.43 28/08/03 +1000, you wrote: >>Thanks to help from Isaac Mehl, limma now supports ArrayVision data. >> The support is in limma 1.1.12. >> >>The data file attached by Isaac is read by >> >> read.maimages("12371987B.csv", source="arrayvision", sep=",") >> >>Cheers >>Gordon

At 22.11 24/09/03 +1000, Gordon K Smyth wrote: > > Hi all! > > > > I tried to use read.maimages to read ArrayVision files as Gordon > > suggested. Unfortunately I get the following: > > > > > read.maimages("12371987B.csv", source="arrayvision", sep=",") > > Error in match.arg(source, c("spot", "spot.close.open", "genepix", > > "quantarray")) : > > ARG should be one of spot, spot.close.open, genepix, quantarray > > > > > > > I've just updated all the packages so I think this is not the problem. > >Yes it is the problem. :-| ops! > The message that you quote is from limma version >1.0.8, i.e., the last official BioC release, rather than from limma 1.2.4 sorry, It was under my eyes. The problem was exactly that. Now read.maimages works perfectly with some file but sometimes fails with others. For example > read.maimages("2706L.csv", source="arrayvision", sep=",") Error in "[.data.frame"(obj, , columns$Gb) : not all specified columns exist Probably it's due to some files problem. Thank you very much. Best, Alessandro

The below is now implemented in limma 1.2.5 which can be downloaded from http://bioinf.wehi.edu.au/limma Gordon >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 / >?m2" are the foreground intensities and that those labeled "Bkgd" are the >background. > >Any other ideas? >Gordon > >EXAMPLE 1 >LINE 1: ,Ctrl,Ctrl,Ctrl,Ctrl,Data,Data,Data,Data, >LINE 2: Spot labels,Median Dens - RFU / ?m2,MAD - RFU / >?m2,Bkgd,sMedianDens,Median Dens - RFU / ?m2,MAD - RFU / ?m2,Bkgd,sMedianDens, >LINE 3: R1 - C1 : 1,29.072,11.878,33.825,0.000,1.247,0.299,0.642,0.605, > >EXAMPLE 2 >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 > >correctly. >Hope it helps. > >Best, >Alessandro > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor