> Date: Mon, 2 Jun 2008 15:26:20 -0700 > From: "Anh Tran" <popophobia at="" gmail.com=""> > Subject: [BioC] Using limma with Agilent array data > To: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > > Hi all, > We've been using Agilent Scanner and Feature Extraction from Agilent. > > I'm wondering if there's a way to import these data into limma. Already answered by Sean Davis. > Out of the > three required input files (GAL file, Targets file, Spot-type file), we only > have GAL file. The GAL file is not required. The targets and spottypes files are created by you, not by Agilent. > FE gives us SHP file and a txt file witn compiled list of > probes and its reading. We are doing 2 color microarray btw. > > If you know any detail, please help us. > > Also, is it possible to group a certain probes together as one entity (they > are expected to have the same result)? If they really are the same probe, then yes, using avereps(). If they are not exactly the same probe, then no. > And is it possible to give a set of > probes as normalizing set for limma (set ratio to 1-1)? You need to read the help file help(normalizeWithinArrays) There is no normalization method in limma for which "set ratio to 1-1" would seem relevant. > I've been looking through the manual but could not find any reference about > Agilent output file. The User's Guide is an overall guide, not the complete manual. For detailed options you need to read the help pages for individual functions. Best wishes Gordon > Thanks all > > -- > Regards, > Anh Tran