[BioC] Anova on 16 CEL files and no annotated data frame(s)

[James W. MacDonald]

Hi Christina,

On 4/10/2012 8:52 AM, Paul, Cristina wrote:
> New to both R and Bioconductor 6 weeks (previous SAS and stat experience (way back when) and other programming languages), googled and have read (books, pdf's etc) but have hit a road block. Have bioconductor case studies,  and the other older springer books for R and gene analysis all open...
>
> I have  been given 16 CEL (AFFY on citrus chip ~30K genes)  files 4 CELs per treatment , one treatment is healthy control. I simply want to perform ANOVA.  I have no annotated data frame there are no subtreatments etc...  it's a very simple comparison subtract healthy and find differences between each trt (up and down regulated genes etc).  All examples I have read are much more complex and have dataframes pre-loaded.
>
> I have normalized and summarized the data sets . both as a group of 16 and by trt, basic code below.
>
>
>> Citruseset<- expresso (Citrus, bgcorrect.method="rma", normalize.method="quantiles", pmcorrect.method="pmonly", summary.method="medianpolish")  ##citrus chip has NA's so other methods used for this produced errors and I could find no go-arounds.
> Design model.matrix file looks like this:
> 1    0        1       0     0
> 2    0        1       0     0
> 3    0        1       0     0
> 4    0        1       0     0
> 5    1        0       0     0
> 6    1        0       0     0
> 7    1        0       0     0
> 8    1        0       0     0
> 9    0        0       1     0
> 10   0        0       1     0
> 11   0        0       1     0
> 12   0        0       1     0
> 13   0        0       0     1
> 14   0        0       0     1
> 15   0        0       0     1
> 16   0        0       0     1
>
> Scatter, box, and volcano plots (which look like blobs) done on each treatment separately show some but not a lot of differentiation between expression. Venn diagrams comparing one trt to the other three (4 total) produced the same number of differences for all but one comparison which we don't believe is correct.
>
> I can't seem to proceed farther  without an annotated data.frame for each CEL or for the batch of them...  and can't find info about how to create one.  Any info or to be pointed to something to read etc would be helpful.

It would be helpful to see your code rather than a description of what 
you have done. For instance, you have a perfectly viable design matrix, 
and have apparently fit a linear model and computed contrasts (else how 
did you get Venn diagrams?). So it isn't clear to me what else you are 
looking to do, or what you need an annotated data frame for.

Please give us your code, along with any errors you may have 
encountered, as well as an indication of how the results/output are not 
meeting your expectations.

Best,

Jim


>
> Thank you,
> Tina Paul
>
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> Cristina Paul
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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