[aroma.affymetrix] Re: CNV analys 28 st SNP 6.0 arrays

2009-06-11 Thread Myriam Peyrard
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

[aroma.affymetrix] Re: CNV analys 28 st SNP 6.0 arrays

2009-06-11 Thread Myriam Peyrard
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:

[aroma.affymetrix] Re: FIRMAGene

2009-06-11 Thread nmcgli...@googlemail.com
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

[aroma.affymetrix] Re: SNPs affecting EXon splicing detection

2009-06-11 Thread sabrina
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

[aroma.affymetrix] Re: FIRMAGene

2009-06-11 Thread Mark Robinson
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:

[aroma.affymetrix] Re: SNPs affecting EXon splicing detection

2009-06-11 Thread Mark Robinson
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

[aroma.affymetrix] Re: CDF files for Affymetrix whole transcript arrays (Gene 1.0, Exon 1.0)

2009-06-11 Thread Mark Robinson
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