[BioC] How do I install custom made CDF in Bioconductor

[James MacDonald]

Hi Ruppert,

I guess I am still a bit confused. Do you have a custom chip that Affy
made for you? If so, they should be able to give you the cdf that comes
with that chip. I don't know how else you have a mixture chip, but
trying to come up with a cdf by hand would be a daunting task to say the
least.

The cdf maps the (X,Y) coordinates of each probe back to the probes
themselves, so making a mixture cdf presupposes some knowledge of where
each probe is located on the chip. I don't know of any way to know this
other than by Affy telling you where they put things.

Is this what you are trying to do, or are you simply trying to combine
data from two different chips somehow?

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
>>> "Ruppert Valentino" <ruppert7 at hotmail.com> 08/22/05 10:57 AM >>>
>Ruppert,
>
>I think you need to give more information before anybody can help. When
>you say custom CDF, does this mean you are using the altcdfenv package,
>or are you somehow modifying the CDF by hand?

Hello Jim,
             Thank you for the reply. Basically I am trying to create a
new 
CDF which has mixture probes from U95ver2a and U133ver2.0. On the Affy
site 
they don't have this so I have to create it myself. I am not sure what
is 
the best way to do this and on what platform. I tried to find a primer
or 
information on how to create custom made CDF but they don't tell you
what 
the structure of the CDF file should be. Also the other issue is I am
using 
R 2.1.1 on Windows but in the manual they say if you are using Windows
then 
you have to do more to creat and upload the CDF environment. Basically I
got 
the CDF file in ASCII format and now trying to create a CDF package that
I 
can use to analyse chips which are mixture of U133 and U95 (not good
idea 
due to a lot of variation but I have to do it).

>In general, you need to run a CDF file through the makecdfenv package
>(using either make.cdf.env() or make.cdf.package()) before it can be
>used. Then if you want to use that cdvenv with your celfiles, you would
>have to read the celfiles into an AffyBatch and then change the cdfName
>slot of the AffyBatch to point to your modified cdfenv.
>
>dat <- ReadAffy()
>dat at cdfName <- "nameofyourcdfenv"
>
>Then proceed as usual.

I will do this thank you. Will this work on R 2.1.1 on Windows or do i
need 
to do it on Linux?

Also what is the minimum requirement for the structure of the CDF file?

Thank you

Ruppert.

>HTH,
>
>Jim
>
>
>
>Ruppert Valentino wrote:
>
> >Hello,
> >         I have created a custom made CDF file and am trying to
install
>that
> >to analyse Affymetrix chip files. Can anyone tell me what format
should 
>the
> >CDF files be in? and when does the CEL file has a CDF file attached
to 
>it,
> >if so how can I update the CEL file data with my custom made CDF?
> >
> >Many thanks
> >
> >Raphael.
> >
> >_______________________________________________
> >Bioconductor mailing list
> >Bioconductor at stat.math.ethz.ch
> >https://stat.ethz.ch/mailman/listinfo/bioconductor
> >
> >
>

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