[BioC] Limma with block and replicate measurement

Gordon Smyth smyth at wehi.EDU.AU
Sun Dec 3 09:36:30 CET 2006

Dear Yanyan

You can use the method described in Section 8.2 (Technical 
Replication) of the Limma User's Guide.

Best wishes

>Message: 9
>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: < at mail.jci.tju.edu>
>Content-Type: text/plain; charset="us-ascii"; format=flowed
>Hi Bioconductors:
>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
>MS. Biostatistician
>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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