Dear Daniel, > Date: Mon, 14 Apr 2008 10:56:13 +0100 > From: Daniel Brewer <daniel.brewer at="" icr.ac.uk=""> > Subject: [BioC] Limma: import files with genes missing > To: bioconductor at stat.math.ethz.ch > Message-ID: <48032A3D.20300 at icr.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1 > > I am trying to use limma to import a series of bluefuse post processed > files. This is the command I am using: > > CGHraw <- read.maimages(CGHFiles,source="bluefuse", > wt.fun=f,annotation=c("ID","NAME","POSITION","CHROMOSOME"),other.col umns=c("NORMFACTOR","COPY > #")) > > The problem is that each of these post processed files only contain the > genes that pass the QA and so different files have different probes. That sounds to me just horrible. Personally, I wouldn't use an image analysis program which prevented me from making my own decisions about the quality of the data. As I've said many times on this list, I think that wholesale spot filtering is almost always a counter-productive practice. > I believe that limma finds all the common probes between the files and > then only imports for them. Actually limma assumes that all files have the same probes. The help file for read.maimages() says "Warning: All image analysis files being read are assumed to contain data for the same genelist in the same order. No checking is done to confirm that this is true. Probe annotation information is read from the first file only." > I would like to do the reverse, importing all the probes that appear in > any file and setting the value where they do not appear to NA. No, limma does not provide any automatic way to do this. If you can get a full gene list, and figure out which probes have been removed from each file, then you could set up a full size matrix, read in each array separately, assign each to right rows and columns, and then you'd have what you want. The best solution by far would be to re-run BlueFuse and tell it to output all the data. > Any way of doing this? > > I have tried importing the files separately and then merging, but that > just uses the the probe list from the first file. Correct. Best wishes Gordon > Thanks > > -- > ************************************************************** > Daniel Brewer, Ph.D. > Institute of Cancer Research > Email: daniel.brewer at icr.ac.uk > **************************************************************

>I have tried importing the files separately and then merging, but that >just uses the the probe list from the first file. Another idea: if you can get a full gene list, then you could construct a dummy RGList object of full length. Then you can do the merge with the dummy as the first array. Still not as good as getting BlueFuse to output all the data. Best wishes Gordon