[BioC] Limma with block and replicate measurement
smyth at wehi.EDU.AU
Sun Dec 3 09:36:30 CET 2006
You can use the method described in Section 8.2 (Technical
Replication) of the Limma User's Guide.
>Date: Fri, 01 Dec 2006 11:52:37 -0500
>From: Yanyan Li <yli at mail.jci.tju.edu>
>Subject: [BioC] Limma with block and replicate measurement
>To: bioconductor at stat.math.ethz.ch
>Message-ID: <18.104.22.168.0.20061201115049.0348ae18 at mail.jci.tju.edu>
>Content-Type: text/plain; charset="us-ascii"; format=flowed
>I am doing Random Block Design for single-color arrays, consider the
>following target frame:
>FileName Exp Trt
>1 1 A
>2 1 B
>3 1 C
>4 1 D
>5 2 A
>6 2 B
>7 2 C
>8 2 D
>9 3 A
>10 3 B
>11 3 C
>12 3 D
>Each mRNA has 3 replicates (same y location and different x location), I am
>not a biology person, I hope I could express clearly.
>Now I want to compare pairwise groups across the 3 experiments, treat Exp
>as block factor (random) and each mRNA is repeated.
>How to incorporate random and repeated effects to lmFit command and also
>Is anyone deal with similar situation or any other suggestions?
>I appreciate all your help.
>Thanks a lot
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>Yanyan Li phone: 215-503-9876, fax: 215-503-3804
>Division of Biostatistics
>Department of Pharmacology and Experimental Therapeutics
>Thomas Jefferson University
>1015 Chestnut St., Suite M100, Mezzanine Floor
>Philadelphia, PA 19107
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