Hi, Mark:
for the Unit_id, does it have to be Ensembl gene ID like ENSMUSG?
Lots of genes do not have ensembl assignment from Affy annotation
file. There are lots of missing annotaions, and I still have not found
any good way to deal with it. Do you have any suggestions?
Thanks
Sabrina
On
Hi Sabrina.
The Unit_ID can be any transcript cluster identifier of your
choice. The easiest may be to use the Affymetrix transcript cluster
identifier itself ... available from:
http://www.affymetrix.com/analysis/downloads/current_exon/MoEx-1_0-st-v1.mm9.probeset.csv.zip
See the
Thanks , Mark!
Can you show me /walk me through how to get a new snp-free CDF ? I
finally got the right version of snp and probe mapping so I am ready
to try it out!
Sabrina
On Jun 6, 3:14 am, Mark Robinson mrobin...@wehi.edu.au wrote:
Hi Sabrina.
Comments below.
On 06/06/2009, at 1:57 AM,
Hi Sabrina.
How about you try and create a 'flat' file like the one described at:
http://groups.google.com/group/aroma-affymetrix/web/creating-cdf-files-from-scratch
Presumably, you will be comfortable with the Exon Array's 'probetab'
file by now and possibly the Affymetrix annotation CSV
Hi Sabrina.
Comments below.
On 06/06/2009, at 1:57 AM, sabrina wrote:
Hi, Mark:
I finally found the SNP data set that is suitable for my case. As I
understand, aroma used RMA to estimate gene level and exon level
intensities. After I estimate gene level (transcript level), I can use
Hi Sabrina.
I have not had to deal with this myself, but I do know that it exists
and I can at least suggest a possible route to exclude affected exons.
Presumably, there is a database (dbSNP?) that tells you the genome
locations of each SNP for your strains. There is also a probe.tab
