[BioC] annotation files for agilent: a bit off-topic

[Francois Pepin]

Hi Weiwei,

I'd assume the last one:

1st is a very old chip
2nd & 3rd are for CGH, not expression
4th is their basic human gene expression.

Keep in mind that they now have 4x44 arrays that use the same non-
control probes but has them in different positions. If the chips were
purchased recently, they are likely the 4x44 ones, as they end up being
a lot cheaper.

The quick and dirty way of finding out: look in the feature extraction
file, you'll see a column that says FeatureExtractor_DesignFileName in
the header. With this should be a file that looks like
014868_D_F_20060807.xml. The first part (014868) says the chip type
(design ID, actually) while the 2nd gives the annotation release date.
Then go to http://www.chem.agilent.com/cag/bsp/array_list.asp and search
in the list. In this case, you'd see this is the 4x44 whole genome mouse
chip. 

There is a bioconductor package for the human whole genome chips:
hgug4112a. This does not include any non-control probes, so it should
work with both the 1x44 and 4x44.

Also, the read.maimages should also grab the gene annotation that is
included in the feature extractor software. They might be out of date,
but it should help you to keep going.

Hope this helps,

Francois

On Tue, 2007-07-17 at 17:43 -0400, Weiwei Shi wrote:
> I am doing the latter now b/c I don't know the answer to the first
> question. The data provider is sloooooowwww in reply.
> 
> On 7/17/07, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> > Weiwei Shi wrote:
> > > Hi, there:
> > >
> > > I knew this is a bit off-topic but hope someone has knowledge to share:
> > >
> > > I found 4 zipped files about annotation from agilent:
> > >
> > > Human 1A(v2)
> > > Human Genome CGH 44A
> > > Human Genome CGH 44B
> > > Human Genome, Whole
> > >
> > > I assume I can use the last one for my arrays but w/o knowing the
> > > difference b/w them, I am not quite sure.
> >
> > You will need to find out what platform your arrays use or do some probe
> > ID matching between your arrays and the annotation packages.  The former
> > is preferred.
> >
> > Sean
> >
> 
>