[BioC] annotations for Codelink arrays

[Diego Diez]

Hi Norman,

On Sep 8, 2006, at 9:14 AM, Normand Richard wrote:


> Hi,
>
> I supervise the gene expression studies currently being conducted at
> Celgene in San Diego, CA.  Adding to our Affymetrix gene expression
> array studies we have begun using the codelink 16-up (16 arrays/slide)
> custom arrays.
> I understand you have written a QC program for codelink arrays.  Is  
> this
> program amenable to the 16-up array format?  Also,  is your QC feature
> similar to the affyQCReport written by Craig Parmen and Conrad  
> Halling?
> I have found the affyQCreport very useful and would like to employ
> something like that program for these codelink arrays as well.
>

It is not a QC program only (or on his own). It can read and pre-process
codelink arrays, exported as text from codelink software and recently I
added experimental code for reading text files exported from excel.  
It has
some quality control features, in the form of density plots, MAplots,  
and
chip image plots. The affyQCReport as I understand it, helps to automate
some of this and other quality plots that could be made, but before you
have to read the data with the affy package though. Currently, a similar
feature is not available in the codelink package. Note, that some of the
QC plots available in the affyQCReport package are specific to the
affymetrix platform, i.e.  depend on the specific design of that
platform, with probe sets of pm and mm probes which are not present  
in the
codelink platform.

Actually, I dont know if the codelink package can manage you data (16- 
up),
because I never tested it. You can try and let me know if it works,  
or you
can sent me two sample files to make the test myself. I dont know  
exactly
the differences in structure of those arrays so this could be as easy as
loading the data and everything working, maybe with some slightly  
changes
in the code or maybe it requires a major rework.

For the annotation question in the subject, there are annotation  
packages
for UniSet and whole genome arrays in the BioC 1.8 release. I will  
try to
add also annotation packages for the adme and immuno arrays in the next
release.

HTH,

Diego.



>
> Thanks for your time in addressing my questions.  Looking forward to
> your reply.
>
> Sincerely,
>
> Normand Richard
> Genomics
> Celgene
> 4550 Towne Centre Ct.
> San Diego, CA 92121
>
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-----------------------------------------------
  Diego Diez, PhD.

  Bioknowledge systems, Kanehisa lab.
  Bioinformatics center,
  Institute for Chemical Research,
  Kyoto University.
  Gokasho, Uji, Kyoto 611-0011 JAPAN.

  e-mail:  diez at kuicr.kyoto-u.ca.jp
  url:     http://web.kuicr.kyoto-u.ca.jp/~diez
  tlf:     +81-774-38-3296
  fax:     +