[BioC] Difficulty with limma contrast matrix creation

[James W. MacDonald]

Hi Brian,

On 4/5/2012 10:54 PM, Brian Gorsuch [guest] 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.

The contrast is dependent on the design matrix, which specifies what 
coefficients you are computing (and hence the interpretation of the 
coefficients). Without knowing your goals and the design matrix you are 
using, it is impossible to give any advice. Perhaps you could elaborate 
a bit?

Best,

Jim


>
> 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
>
> --
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>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099