Bug in gcrma_0.4.0?
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@james-w-macdonald-5106
Last seen 7 hours ago
United States
Running gcrma 0.4.0 on a WinXP box with R-1.7.1, I get odd results when selecting the empirical bayes background correction (U133A chips). I tried with and without triple.goal, and the results are the same. Attached are some MA plots of the same two chips processed using rma and gcrma using empirical bayes and mle background estimation. Not sure if the mail server is stripping attachments due to our recent experiences with sobig.F, so I also cc'ed to Rafael Irizarray (sorry for the double email Rafael...). Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 -------------- next part -------------- A non-text attachment was scrubbed... Name: MvA_gcrma_mle.png Type: image/png Size: 10503 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20030822/53a3190e/MvA_gcrma_mle-0001.png -------------- next part -------------- A non-text attachment was scrubbed... Name: MvA_no_triplegoal.png Type: image/png Size: 12389 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20030822/53a3190e/MvA_no_triplegoal-0001.png -------------- next part -------------- A non-text attachment was scrubbed... Name: MvA_rma.png Type: image/png Size: 10503 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20030822/53a3190e/MvA_rma-0001.png -------------- next part -------------- A non-text attachment was scrubbed... Name: MvA_with_triplegoal.png Type: image/png Size: 12971 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20030822/53a3190e/MvA_with_triplegoal-0001.png
Microarray Cancer gcrma Microarray Cancer gcrma • 751 views
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