Hi Michelle,
I've just added vignette 'Paired parent-specific copy-number
segmentation (Paired PSCBS) (low-level API after AS-CRMAv2)':
http://aroma-project.org/vignettes/PairedPSCBS-lowlevel
See if that helps
/Henrik
On Fri, Nov 11, 2011 at 1:02 PM, Michelle wrote:
> Dear aroma community,
Thank you very much for the detailed explanation.
Hoon
On Nov 11, 2:11 pm, Henrik Bengtsson wrote:
> Hoon, thanks for the note. Yes, there is a discrepancy in how clever
> the methods are. Basically the AromaUnitCnBinarySet methods go
> further in trying to figure out what annotations are need
Dear aroma community,
We are trying to do paired CBS analysis on some Affy SNP 6.0 data
using the R package "PSCBS", but not sure how to extract the total CN
and BAF values from the raw array files (.CEL) into the needed format
(pasted below). It seems aroma.affymetrix has some relevant functions
Hoon, thanks for the note. Yes, there is a discrepancy in how clever
the methods are. Basically the AromaUnitCnBinarySet methods go
further in trying to figure out what annotations are needed. FYI,
contrary to data set directories, the name of the chip type directory
will never have tags, which
Dear Pierre,
Thank you very much for your prompt reply.
FYI. I processed the Affymetrix SNP 6.0 data as follows:
-
dataSet <-"AffyTestData"
chipType <-"GenomeWideSNP_6"
verbose <- Arguments$getVerbose(-8, times
Ok, so you have rather old versions running. Start by updating the XML
package, retry and report back:
http://cran.r-project.org/web/packages/XML/index.html
Also, if it still gives and error, what does the following return:
> digest(raw)
[1] "ecfee3f93033dbbf4a25fd27195ff0e9"
/Henrik
On Fri,
Hi wisekh6,
Although you don't give the code you used to process this data, from
what you report it looks like you initially processed your data set
using the "full" chip type. See below.
On Fri, Nov 11, 2011 at 7:22 AM, wisekh6 wrote:
> Dear all,
>
> After processing Affymetrix GenomeWide SNP
Hi Henrik,
Thanks for your help in tracking the problem.
I tested your lines of code and it worked up until the point of the "
ftr <- readFooter(ufl); " command, here I paste the results below:
> ufl <- AromaUflFile$byChipType("Mapping250K_Sty", tags="na31,HB20101007");
> print(getFileSize(ufl))
