Hi,

I would like to use MapMan on data from Arabidopsis Gene 1.0 ST Arrays, but an according mapping file is not available. The format of my probe set IDs is e.g. 13341578 and does not match the format of the ATH1mapping files. Can you implement a new mapping to MapMan?
Thanks for your help,

Maik Bartelheimer

Hi Maik,

the problem is that currently there seems to be no CDF environment for this chip type
available from the bioconductor web site - hence RobiNA fails when trying to obtain this
information. It might be possible to generate a CDF environment on the fly within the
RobiNA affy analysis workflow as long as you have the corresponding CDF file - this
is usually availble via the Affymetrix web site (for non-private chip designs).

Analysing the ST arrays involves a different preprocessing that the standard arrays
(in case you are versed in R have a look at: http://www.bioconductor.org/packages/2.11/bioc/html/xps.html)
Incorporating this will require some time for adapting the scripts underlying RobiNA
and the GUI.

So, i fear, for now the analysis will only be possible directly using R.

best greetings,
Marc

After rereading your message i realize that i did answer a different question than the one you'd
asked! My bad.

You had actually asked for a mapping file for the array - we can generate such a file automatically
if you can provide the sequences of the genes the probes were targeted against or a table assigning
each probe ID to the AGI code of the corresponding arabidopsis gene.

best greetings,
Marc

Hi Marc,
I'm trying to use GenePattern to analyse my Arabidopsis Gene 1.0 ST array data, but as you said the .CDF is not available.
Do you know how doI get it? Please assume that I know very little about how to create the .CDF myself!
Thanks!
Rodrigo

Hi Rodrigo,

first, I want to let you know that we do now have a mapping file for the AraGene ST data
that can be downloaded from the MapManStore or directly from within the MapMan
application by right-clicking "Mappings"-->"new"-->"download".

Concerning your question - the data structure of the ST arrays differs from the standard
GeneChip arrays - there is no CDF file for these arrays which means that the analysis
in R requires some different/additional steps and the current version of RobiNA cannot be
used to analyse ST data. The next major version of RobiNA will include ST-Chip analysis
but is not ready for release yet.

Sorry for the inconvenience

cheers,
Marc