[BioC] Difficulty with limma contrast matrix creation

[Brian Gorsuch [guest]]

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(): 

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