If you are stuggling perhaps try looking at the "createContrastMatrix()"
function in the puma package, that can in many cases do this automatically.
http://rss.acs.unt.edu/Rdoc/library/puma/html/createContrastMatrix.html

Paul

On Fri, Apr 6, 2012 at 3:54 AM, Brian Gorsuch [guest] <
guest@bioconductor.org> wrote:

>
> Dear members,
> I would be very grateful for any assistance.  I am having difficulites
> with creating a contrast matrix for my data in limma, as well as then
> applying the matrix to the modeled data to compute statistics, and the
> output for such.
>
> I have included my targets.txt file.  I was attempting to follow the
> tutorial "single channel analysis of agilent microarray data with limma" by
> the mattick lab.  Unfortunelty mine is not a simple 2x2 factorial matrix.
>
> Thank you very much for any suggestions, and your time in doing so.
>
> FileName        Genotype        Treatment       Time.d  Sample
> US45102885_252665511314_S01_GE1-v5_95_Feb07_1_4.txt     C2fb    STZ     4
>       V237
> US45102885_252665511314_S01_GE1-v5_95_Feb07_1_3.txt     C2fb    STZ     4
>       V236
> US45102885_252665511333_S01_GE1-v5_95_Feb07_1_1.txt     C2fb    STZ     4
>       V238
> US45102885_252665511333_S01_GE1-v5_95_Feb07_1_2.txt     C2fb    STZ     14
>      V242
> US45102885_252665511333_S01_GE1-v5_95_Feb07_1_4.txt     C2fb    STZ     14
>      V244
> US45102885_252665511333_S01_GE1-v5_95_Feb07_1_3.txt     C2fb    STZ     14
>      V243
> US45102885_252665511310_S01_GE1-v5_95_Feb07_1_1.txt     WT      CBS     4
>       V218
> US45102885_252665511310_S01_GE1-v5_95_Feb07_1_2.txt     WT      CBS     4
>       V219
> US45102885_252665511310_S01_GE1-v5_95_Feb07_1_3.txt     WT      CBS     4
>       V220
> US45102885_252665511310_S01_GE1-v5_95_Feb07_1_4.txt     WT      CBS     14
>      V227
> US45102885_252665511311_S01_GE1-v5_95_Feb07_1_1.txt     WT      CBS     14
>      V228
> US45102885_252665511311_S01_GE1-v5_95_Feb07_1_2.txt     WT      CBS     14
>      V229
> US45102885_252665511311_S01_GE1-v5_95_Feb07_1_3.txt     WT      STZ     4
>       V224
> US45102885_252665511311_S01_GE1-v5_95_Feb07_1_4.txt     WT      STZ     4
>       V225
> US45102885_252665511312_S01_GE1-v5_95_Feb07_1_1.txt     WT      STZ     4
>       V226
> US45102885_252665511312_S01_GE1-v5_95_Feb07_1_2.txt     WT      STZ     14
>      V231
> US45102885_252665511312_S01_GE1-v5_95_Feb07_1_3.txt     WT      STZ     14
>      V239
> US45102885_252665511312_S01_GE1-v5_95_Feb07_1_4.txt     WT      STZ     14
>      V240
>
>
>  -- output of sessionInfo():
>
> we
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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>



-- 
Paul Geeleher (PhD Student)
School of Mathematics, Statistics and Applied Mathematics
National University of Ireland
Galway
Ireland
--
www.bioinformaticstutorials.com

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