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Paul, Cristina
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50
@paul-cristina-5211
Last seen 9.6 years ago
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.
Thank you,
Tina Paul
Whether you think you can or think you can't - Your're right...
Henry Ford
Cristina Paul
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