would be a practical solution to mapping all the regions from regions.xls.
What do people do for this kind of mapping? Do you have any suggestions? I
could probably use biomaRt for this, but what would you suggest for mapping
the regions to Affy IDs and locus/EntrezGene? Thanks.
-Andrew Smit
akes quite a while (and is the
majority of the overall processing time taken), which generates the
regions.xls file. Am I missing any
intermediate result files for this that could speed it up? Thanks again for
your help.
On Tuesday, March 4, 2014 8:40:26 PM UTC-5, Henrik Bengtsson wrote:
>
>
of the arrays and run this on the subset,
then run it again on a single CPU for all the arrays. And I'm doing the
parallelization using the multicore package's mclapply.
Does this seem okay or would you recommend any changes?
thanks,
Andrew Smith
On Friday, December 3, 2010 1:18:23
0.0 RCurl_1.95-3 Rsamtools_1.10.2
RSQLite_0.11.2
[13] rtracklayer_1.18.2 stats4_2.15.2 tools_2.15.2 XML_3.95-0.1
[17] zlibbioc_1.4.0
On Monday, March 4, 2013 3:24:13 PM UTC, Andrew Beggs wrote:
>
> Hi
>
> I have multiple Affy methylation tiling arrays, (i
e limma to construct a model, but I can't see how limma
could be applied to the dataset output by regionStats
Has anyone any experience with his?
BW
Andrew
--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output
Henrik, thanks again. It's working now.
On Monday, June 18, 2012 4:58:19 PM UTC-4, NT_CMU wrote:
>
> Hi
>
> I'm trying to run the command "doCRMAv2", and i get these errors. Let me
> know what the problem is, if any of you have encountered this before. I
> thought i did not have some library ins
1:51:49 PM UTC-4, Henrik Bengtsson wrote:
>
> Following the troubleshooting of annotationData/ on
> http://aroma-project.org/troubleshooting/DirectoryStructures using
> chipType <- "GenomeWideSNP_6", what does print(list.files(path=path))
> output?
>
> /Henrik
>
>
I feel it might be better to post my question in this thread, as I have
encountered the same error.
I've downloaded ufl, ugp, and acs files from AROMA SNP6 webpage, and the
Full cdf file from Affymetrix. And I still got the same kind error NT_CMU
got for "getGenomeInformation".
Could you plea
