[BioC] LIMMA - fold change direction?

Jenny Drnevich drnevich at illinois.edu
Thu Jul 17 18:49:20 CEST 2008

Hi Glyn,

Your design matrix has the first array of the dye-swap pair as 
positive, which has Day27 in the Cy5. Because the M values you're 
testing are log2(R/G), yes a positive M value means upregulated in 
the Day27 samples. Two other suggestions:

1. If you only have 3 biological replicates, the dye-swaps are 
technical replicates. Your analysis is acting as if you had 6 
biological replicates. See the limma vignette limmaUsersGuide() , 
section 8.2 to how to properly account for technical replicates. They 
have an example almost identical to your experiment (2 bio reps with 

2. It would be better to call your samples Day17 and Day27 - if you 
should ever have to use them for column names, R & limma can be funny 
about names that begin with a number.


At 10:42 AM 7/17/2008, Glyn Bradley wrote:
>Hi all
>3 bio replicate and dye swap cDNA array experiment comparing 17day and
>27day samples being analyzed with limma
>targets file:
>"Name"  "FileNameCy3"   "FileNameCy5"   "Cy3"   "Cy5"
>         "1-Cy3-Ac-17d.txt"      "1-Cy5-Ac-27d.txt"      "17day" "27day"
>         "2-Cy3-Ac-27d.txt"      "2-Cy5-Ac-17d.txt"      "27day" "17day"
>         "3-Cy3-Ac-17d.txt"      "3-Cy5-Ac-27d.txt"      "17day" "27day"
>         "4-Cy3-Ac27d.txt"       "4-Cy5-Ac17d.txt"       "27day" "17day"
>         "5-Cy3-Ac17d.txt"       "5-Cy5-Ac27d.txt"       "17day" "27day"
>         "6-Cy3-Ac27d.txt"       "6-Cy5-Ac17d.txt"       "27day" "17day"
>so after
>RG <- read.maimages(files, source="imagene")
>MA <- normalizeWithinArrays(RG)
>fit <- lmFit(MA, design)
>what direct are the fold changes I get out in
>does a positive FC mean up regulated in the 27day sample?
>(ps I would've found it useful if 'coefficients' were labelled logFC
>all the way through. But that might be due to my lack of stats
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>Search the archives: 

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801

ph: 217-244-7355
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e-mail: drnevich at illinois.edu

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