I am struggling to get data from Agilent cDNA arrays into BioConductor. It seems to me much easier to get the data in affy's normalize.loess() than in the other cDNA array packages. Given that "one who get a bargain get what he pays for", does anyone has comments, recommendations or warnings to share about using an Affy normalization procedure on cDNA data? Thanks, Joel M. Malard, Ph.D. Scientist IV Pacific Northwest National Laboratory Battelle Boulevard, PO Box 999 Mail Stop K1-85 Richland, WA 99352 "I love the audacity of those who have everything to loose from it; the moderation of those who have nothing to gain from it." Rostand, Jean (1894-1977) [[alternative HTML version deleted]]

Why not just use Limma and the corresponding tools? It's FAR easier that way. That way you actually get what you pay for, rather than far less... "Malard, Joel M" <jm.malard@pnl.gov> writes: > I am struggling to get data from Agilent cDNA arrays into BioConductor. > It seems to me much easier to get the data in affy's normalize.loess() > than in the other cDNA array packages. > > Given that "one who get a bargain get what he pays for", does anyone has > comments, recommendations or warnings to share about using an Affy > normalization procedure on cDNA data? > > Thanks, > > Joel M. Malard, Ph.D. > Scientist IV > Pacific Northwest National Laboratory > Battelle Boulevard, PO Box 999 > Mail Stop K1-85 > Richland, WA 99352 > > "I love the audacity of those who have everything to loose from it; the > moderation of those who have nothing to gain from it." Rostand, Jean > (1894-1977) > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- Anthony Rossini Research Associate Professor rossini@u.washington.edu http://www.analytics.washington.edu/ Biomedical and Health Informatics University of Washington Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}}

Thank you for pointing this out. I had not seen that read.maimages() can process 'agilent' files and thought all the data structures had to be filled in manually. Best wishes, Joel -----Original Message----- From: A.J. Rossini [mailto:rossini@blindglobe.net] Sent: Friday, September 17, 2004 12:53 PM To: Malard, Joel M Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] Loess normalization for Agilent chips Why not just use Limma and the corresponding tools? It's FAR easier that way. That way you actually get what you pay for, rather than far less... "Malard, Joel M" <jm.malard@pnl.gov> writes: > I am struggling to get data from Agilent cDNA arrays into > BioConductor. It seems to me much easier to get the data in affy's > normalize.loess() than in the other cDNA array packages. > > Given that "one who get a bargain get what he pays for", does anyone > has comments, recommendations or warnings to share about using an Affy > normalization procedure on cDNA data? > > Thanks, > > Joel M. Malard, Ph.D. > Scientist IV > Pacific Northwest National Laboratory > Battelle Boulevard, PO Box 999 > Mail Stop K1-85 > Richland, WA 99352 > > "I love the audacity of those who have everything to loose from it; > the moderation of those who have nothing to gain from it." Rostand, > Jean > (1894-1977) > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- Anthony Rossini Research Associate Professor rossini@u.washington.edu http://www.analytics.washington.edu/ Biomedical and Health Informatics University of Washington Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}}