Dear John, Yes, Feature Extraction combines the two scans into a single results file. It turns out that the results file format had changed because when our scanner was serviced the settings were changed. I realize now that I would have had to specify the column headings regardless of this issue because I would like to use the median signal measurements and the column definition in the read.maimages function in limma (I'm using v2.16.4) source="agilent" is G = "gMeanSignal",Gb = "gBGMedianSignal", R = "rMeanSignal", Rb = "rBGMedianSignal". Thanks for your quick reply and help, Ilsa -----Original Message----- From: John Fernandes [mailto:jfernand@stanford.edu] Sent: Wednesday, February 04, 2009 4:10 PM To: Coleman, Ilsa Cc: Sean Davis Subject: Re: [BioC] read.maimages(limma) source="agilent" updated for 20-bitscanner? In my experience, the Agilent Feature Extraction software creates a single data file by combining the high/low scans so you'd have one data file regardless of whether you did a single scan or a high/low double scan. Are you using Agilent Feature Extraction on the tiffs generated by the scanner? John -------------------------------------------------- From: "Sean Davis" <seandavi@gmail.com> Sent: Wednesday, February 04, 2009 3:59 PM To: "Coleman, Ilsa" <icoleman at="" fhcrc.org=""> Cc: <bioconductor at="" stat.math.ethz.ch=""> Subject: Re: [BioC] read.maimages(limma) source="agilent" updated for 20-bitscanner? > On Wed, Feb 4, 2009 at 6:39 PM, Coleman, Ilsa <icoleman at="" fhcrc.org=""> wrote: > >> Hi, >> I can read in 2-color Agilent data from 16-bit scans (Agilent >> Technologies Scanner G2505B) using read.maimages(limma) >> source="agilent" but for some reason cannot read in data files from >> 20-bit scans (Agilent Technologies Scanner G2505C). This probably >> has to do with the fact that the 20-bit scans no longer require two >> scans (low and high) so there are fewer data columns in these files. >> Has anyone else had this problem and is there a plan to update the >> read.maimages(limma) function? >> > > Hi, Ilsa. You can specify the columns to read using read.maimages. > See the help page for a great deal of detail. > > Sean > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor