[BioC] outlier probes detection
Guido.Hooiveld at wur.nl
Tue May 8 13:22:07 CEST 2012
If the affected area is relatively small (less than 5-10% of total area) we usually ignore these scratches/bubbles (because each probeset is comprised of multiple probes, and the robust summarization methods usually used within RMA (median polish or M-estimator) are able to handle these outliers pretty well).
Alternatively, the package 'Harshlight' offers options to correct for various types of artefacts.
Guido Hooiveld, PhD
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
Biotechnion, Bomenweg 2
NL-6703 HD Wageningen
tel: (+)31 317 485788
fax: (+)31 317 483342
email: guido.hooiveld at wur.nl
From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of andrea.grilli at ior.it
Sent: Tuesday, May 08, 2012 12:15
To: bioconductor at r-project.org
Subject: [BioC] outlier probes detection
I'm performing an analysis on HGU133plus2 arrays with 40 samples; looking at their surface with "affyPLM" package, I've seen a couple of arrays with small scratches and one more with a small bubble. Because I don't want to exclude these arrays (according to Murphys' law 2 on 3 belong to the class with less samples), I want to detect those probes and to exclude them.
I was thinking in some outlier detection method, but because I'm new to this problem I don't know if this is the right method and which packages can be appropriate (did some research but I've no clear idea).
Any help is really appreciated,
Dr. Andrea Grilli
andrea.grilli at ior.it
Laboratory of Experimental Oncology,
Development of Biomolecular Therapies unit, Rizzoli Orthopaedic Institute Codivilla Putti Research Center via di Barbiano 1/10
40136 - Bologna - Italy
Bioconductor mailing list
Bioconductor at r-project.org
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
More information about the Bioconductor