exclude spots with zero weight 0 from lmfit toptable list in limmaGUI
0
0
Entering edit mode
@christine-voellenkle-3067
Last seen 10.2 years ago
Dear BioConductor mailing list! I perform 2 color hybridization with Exiqon slides, where each mir has 4 replicates. I compare a rather small number of slides (from 2 up to 6 biologial replicates for each treatment). For analysis of the data I am using the R-2.8, the limma package and its interface limmaGUI. That's what I do: loading Genepix files background correction (normexp, cutoff=10), setting the GenePix Weightings: unflagged= 1, everything else= 0, within (global loess) and between (Scale) array normalization. To obtain the statistics for differential expression I choose the "least squares" linear model fit and the calculation of Duplicate correlation. Seems to work well, the problem is, that not always all 4 replicates of one mir are "unflagged". It can happen that on the same slide only 2 or 3 replicates are unflagged, or that on one slide all of the 4 replicates are flagged bad, but on the other slides all replicates for the same mir are unflagged. If I understood well, setting the weights only means that the intensities from spots with zero weight do not influence the normalization. How do I exclude the spots with zero weigths from the further calculations of the linear model fit, is there a way in limmaGUI to exlude the bad spots from the toptable list? Thanks a lot in advance. Greetings, Christine Dr. Christine Völlenkle, Ph.D. Research Laboratories-Molecular Cardiology I.R.C.C.S. Policlinico San Donato Via R. Morandi, 30 20097 S. Donato M.se (MI) Italy Phone: +39 02 52774 683 (lab) +39 02 52774 533 (office) Fax: +39 02 52774 666 email: christine.voellenkle@gmail.com [[alternative HTML version deleted]]
Normalization limma limmaGUI Normalization limma limmaGUI • 1.0k views
ADD COMMENT

Login before adding your answer.

Traffic: 682 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6