OK, nice to hear, about the warnings.
Then I do:
display(ce)
and started to look in my different samples, all chromosomes.
Seems that there is not a single CNV variation there?
I did the normalization as non-paired sample sets, with average calculated
with all samples:
cbs - CbsModel(cesN)
Is
Moreover, chrom 1 and 2, in all samples, seems not to have been done, (in
grey shade when browsing acrross chromosomes and samples.
Myriam
-Original Message-
From: Myriam Peyrard [mailto:myriam.peyr...@ki.se]
Sent: den 11 juni 2009 10:09
To: 'aroma-affymetrix@googlegroups.com'
Subject:
Hello,
I have two questions regarding FIRMAGene:
1. The same as the first in this thread: using the code from sup3.r
when I try to load the FIRMAGene library or execute the FIRMAGene
command I get the following errors:
library(FIRMAGene)
Error in base::library(...) : there is no package
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 Nick.
At present, FIRMAGene is not actually part of the aroma.affymetrix
project, although it makes use of it. So, I will reply to this off
the aroma.affymetrix mailing list, except to say that FIRMAGene is now
hosted by R-forge. See the following link for details:
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
Hi Dick.
(I've copied the aroma.affymetrix list in case others have the same
question).
I remember doing an update *late* last year (don't remember exactly
when) and recreating the CDFs --- the contents were identical to
previous ones. That is, the Affymetrix annotation (at least how
