Hi Achilleas,

Thanks for that yes that is what I was expecting to see. Thank you.
Can you shed any light on how I should define the contrast matrix?

Thanks

E

From: Achilleas Pitsillides [mailto:anp4r@virginia.edu]
Sent: 26 May 2011 14:55
To: elliott harrison
Cc: bioconductor@r-project.org
Subject: Re: [BioC] paired sample LIMMA

Hi,

In your current design the variables MouseX ( for X in {2,3,4})   encode the difference of MouseX from Mouse1, i.e. the intercept is Mouse1. If you want to have Mouse1 be explicit then just change:
pairdesign <- model.matrix(~MouseNo+Cycle+State, ref = "ref")
to
pairdesign <- model.matrix(~0+MouseNo+Cycle+State, ref = "ref")
I hope this helps.

cheers,
Achilleas
On Thu, May 26, 2011 at 9:27 AM, elliott harrison <e.harrison@epistem.co.uk<mailto:e.harrison@epistem.co.uk>> wrote:
Hi BioC,

I have a question regarding the output of a LIMMA. I have 2 colour data with a constant reference.
Some googling lead me to some references that as I have a constant dereference I can set up a paired comparison as in the limma example.


I have the following targets file

> targets
      Filename  Cycle  State MouseNo
File1     File1 Cycle1 State1       1
File2     File2 Cycle1 State1       2
File3     File3 Cycle1 State1       3
File4     File4 Cycle1 State1       4
File5     File5 Cycle1 State2       1
File6     File6 Cycle1 State2       2
File7     File7 Cycle1 State2       3
File8     File8 Cycle1 State2       4
File9     File9 Cycle2 State1       1
File10   File10 Cycle2 State1       2
File11   File11 Cycle2 State1       3
File12   File12 Cycle2 State1       4
File13   File13 Cycle2 State2       1
File14   File14 Cycle2 State2       2
File15   File15 Cycle2 State2       3
File16   File16 Cycle2 State2       4

Try to set up the design like this:

MouseNo <- factor(targets$MouseNo)
Cycle <- factor(targets$Cycle, levels=c("Cycle1","Cycle2"))
State <- factor(targets$State, levels=c("State1","State2"))
pairdesign <- model.matrix(~MouseNo+Cycle+State, ref = "ref")

> pairdesign
  (Intercept) MouseNo2 MouseNo3 MouseNo4 CycleCycle2 StateState2
1            1        0        0        0           0           0
2            1        1        0        0           0           0
3            1        0        1        0           0           0
4            1        0        0        1           0           0
5            1        0        0        0           0           1
6            1        1        0        0           0           1
7            1        0        1        0           0           1
8            1        0        0        1           0           1
9            1        0        0        0           1           0
10           1        1        0        0           1           0
11           1        0        1        0           1           0
12           1        0        0        1           1           0
13           1        0        0        0           1           1
14           1        1        0        0           1           1
15           1        0        1        0           1           1
16           1        0        0        1           1           1


Mouse 1 has vanished in the design and the resultant MArrayLM object from lmFit. What am I doning wrong.

Also what would be the syntax for specifying contrasts for contrasts.fit in this example.

Thanks

Elliott

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