[BioC] assist in constructing a design matrix & contrast matrix for Illumina microarray

[James W. MacDonald]

Hi Maria,

Maria Dolores Serafica wrote:
>    Dear Bioconductor Staff,
> 
> 
>    I sent this email on Oct 27 & would like to know if it was received and if
>    someone can help.
> 
> 
>    I am analysing Illumina Beadchips (HumanWG6) for 42 SAMPLES.
>    Experimental design: (factorial) time course, samples grown on 4
>    media; have zero control sampled at onset only[ one way multigroup
>    analysis]; 2-3 reps per treatment.
> 
>    I used the lumi script by Pan Du et al (2009) for preprocessing
>    and normalisation . This part  was okay. The samples were subsetted
>    and are R objects.
> 
>    SAMPLE 1 REFERENCE SAMPLE  DAY 0 (triplicate)
>    SAMPLE 2 MEDIA A DAY 7 (triplicate)
>    SAMPLE 3 MEDIA A DAY 14 (triplicate)
>    SAMPLE 4 MEDIA A Day 30 (triplicate)
>    SAMPLE 5 MEDIA A DAY60  (singleton)
>    SAMPLE 6 MEDIA A DAY90 (replicates)
>    SAMPLE 7 MEDIA B DAY 7 (triplicate)
>    SAMPLE 8 MEDIA B DAY 14 (triplicate)
>    SAMPLE 9 MEDIA B DAY 30 (triplicate)
>    SAMPLE 10 MEDIA B DAY60 (singleton
>    SAMPLE 11 MEDIA B DAY 90 (TRIPLICATE)
>    SAMPLE 12 MEDIA C DAY 7 (REPLICATES)
>    SAMPLE 13 MEDIA C DAY 14 (REPLICATES)
>    SAMPLE 14 MEDIA C DAY 30 (REPLICATES)
>    SAMPLE 15 MEDIA D DAY 7 (REPLICATES)
>    SAMPLE 16 MEDIA D DAY 14 (REPLCATES)
>    SAMPLE 17 MEDIA D DAY 30 (REPLICATES)
>    SAMPLE 18 MEDIA D (DAY 90 (REPLICATES
> 
>    This is a differentiation experiment.
> 
>     I tried the lumi script using the modified limma (PanDu et al 2009) based
>    on the Barnes subset data but the script does not apply to my experimental
>    set up.  Can someone assist me in making a design matrix and a contrast
>    matrix.
> 
>    I am new to R and would like to use limma for identifying differentially
>    expressed genes.  I have read the limma users guide(Gordon Smyth), LAB4
>    limma 2005, James MacDonald's BioC 2009.
> 
>    The contrasts (comparisons) I am looking for:
>    a. differential gene expression of each sample WITH the reference
>    b. early differentiation genes as affected by media, time and both
>    c. late differentiation genes as affected by media or both.

It's good that you have done some homework and are trying to learn how 
to do the analysis, but in the end you are asking somebody to do your 
work for you (for free), and it's not likely that you will get many 
people who want to do that.

If the examples you have read are not sufficient to help you do the 
analysis, I would suggest trying to find a local statistician to 
collaborate with, or at least to give you some help.

Best,

Jim


> 
> 
>    Sincerely,
> 
>    Maria
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826