[aroma.affymetrix] Distribute Aroma Objects As Rdata

Hi, Since the package caches everything to disk, I'm wondering if it is possible to save a group of Aroma objects as an .Rdata object, to be used as examples within a user manual without the manual's reader having to setup the directory structure and download each file manually? Thanks. --

[aroma.affymetrix] Relative Copy Number Analysis

of the functions that appear in the total copy number vignette. Can anyone share a workflow for a relative analysis ? -- Dario Strbenac Research Assistant Cancer Epigenetics Garvan Institute of Medical Research Darlinghurst NSW 2010 Australia -- When reporting

Re: [aroma.affymetrix] Problem with read CDF files

http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ -- Dario Strbenac Research Assistant Cancer Epigenetics Garvan Institute of Medical

Re: [aroma.affymetrix] Parameters Sent To DNAcopy Functions

@googlegroups.com Hi. On Wed, Sep 29, 2010 at 8:00 PM, Dario Strbenac d.strbe...@garvan.org.au wrote: Hello, I remember reading a while ago that you can pass in additional parameters to CbsModel, and they will get passed onto DNAcopy functions. However, it doesn't seem to be working for me. I don't

[aroma.affymetrix] Mouse430_2 CDF Location

Hi, I'd like to download the CDF of Mouse430_2, but the webpage for it just shows an example of how to register it. http://aroma-project.org/node/33 How can I get myself a copy of the CDF file ? Thanks, Dario. -- Dario Strbenac Research Assistant

[aroma.affymetrix] append() for celSets

Hello, The append function works in a strange way because it modifies its first argument, as well as the result variable. Unusual for R, anyway. It would be nice to document this behaviour. Notice in the example that both combined and celSet have been expanded to 12 elements. cdf -

[aroma.affymetrix] Function Clash With IRanges

When loading aroma.affymetrix, then calling a function that has require(GenomicRanges) in it, that has AromaCellPositionFile $byChipType(getChipType(cdf)), I get an error because IRanges has a trim method too, and the aroma method eventually calls trim(tags). Should this be R.oo::trim(tags) in

Re: [aroma.affymetrix] Function Clash With IRanges

Thanks for this. I tried it before, but I think the reason that it didn't work for me previously is that I didn't start a new R session. It works now that I did it in a new session. - Dario. -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the

[aroma.affymetrix] Affine Normalisation

The documentation says : This method will both remove curvature in the M vs A plots that are due to an affine transformation of the data. What is the other issue it is referring to apart from curvature, but is not mentioned ? Or maybe the word 'both' is erroneously there ? -- When reporting

RE: [aroma.affymetrix] Affy methylation tiling arrays - comparison of multiple groups

locations. Smoothing and aggregating is the way to go. -- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output

RE: [aroma.affymetrix] how to get differential region after MatSmoothing?

Hello, In the Bioconductor package Repitools, there is a function called regionStats. That will do what you need. You can find out more information at http://www.bioconductor.org/packages/release/bioc/html/Repitools.html From: