[BioC] Human whole genome Codelink arrays and paired analysis

[Diego Diez]

Hi Matt,

you can use the codelink package (that I maintain) to background  
correct and normalize your dataset. For statistical analysis, if you  
are planning to use for instance, limma, you can use lmFit() with a  
matrix of intensities that are stored in the Ni slot in the  
normalized object. For example:

# read and pre-processing.
foo <- readCodelink()
foo <- bkgdCorrect(foo)
foo <- normalize(foo)

# statistical analysis.
...
# linear model step:
fit <- lmFit(foo$Ni, ...)
...

You can also use the annotation package for the human whole genome  
chips -available from bioconductor - for reporting a list of  
differentially expressed genes.

I would recommend you to read the codelink vignette for details. If  
you have any doubt don't hesitate to ask here though. For the  
statistical part of you mail I'll let others more experienced than me  
to answer it but a good starting point would be to read the limma  
user's guide.

Best,

Diego

On Oct 22, 2007, at 8:21 PM, Matthew Neville wrote:

> Hi,
>
> This is my first post to this forum and I am right at the bottom of
> the learning curve when it comes to R but I have a few initial
> questions.
>
> Does anyone have experience with analysing Codelink arrays in R,  I
> see there is a normalisation program which improves on the Codelink
> software but are there any other considerations I need to take into
> account ?.
>
> Also,  my dataset is based on biopsies from 12 individuals taken at 3
> time points after they start taking a drug so when looking for
> differentially expressed genes my most powerful tests would be
> paired, i.e. paired ttest or repeated measures ANOVA equivalents.
> However, most analyses seem to be unpaired, does anyone have any
> advice?.
>
> many thanks in advance
>
> Matt
>
> Matt Neville D.Phil
> Oxlip Group
> Oxford Centre for Diabetes,Endocrinology and Metabolism
> Churchill Hospital
> Old Road
> Headington
> Oxford
> OX3 7LJ
> matthew.neville at oxlip.ox.ac.uk
> TEL: 01865 857289
> FAX: 01865 857217
>
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--
Dr. Diego Diez
Bioinformatics center,
Institute for Chemical Research,
Kyoto University.
Gokasho, Uji, Kyoto 611-0011 JAPAN
diez at kuicr.kyoto-u.ac.jp