Hi Fred.
Sorry for the slow reply.
Perhaps this thread answers your question:
http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/04c4b6ee767ff666
... and of course checking that you don't have objects in your current
workspace that are consuming a large amount of RAM.
Cheer
Check you parentheses;
r <- log2(extractMatrix(rs),cells=ind,verbose=verbose)
You probably mean:
r <- log2(extractMatrix(rs,cells=ind, verbose=verbose))
FYI, for troubleshooting, it is also better to do:
r <- extractMatrix(rs,cells=ind, verbose=verbose)
r <- log2(r)
-H
On Tue, Aug 25, 2009
Hi Jen.
I can't tell what's happening.
Can you run this from a fresh R session, give your sessionInfo(), an
output of traceback() when you get the error and include the whole
script and the output?
One thing I wonder is if there are other results files kicking around
that are interfering,
Hello all,
Thanks for including the MAT implementation into aroma - works very
nicely.
I have a quick and probably very simple question re the results, which
look like this:
chr118996 0.189100
is this the location of the peak?, as the probes are 25bp in length?
Many thanks
Lavinia.
--~--~-
Such a simple question, I've answered it myself! - the location is the
start of the probe (checked the .bed file).
thanks.
Lavinia.
On Aug 26, 8:59 am, Lavinia Gordon wrote:
> Hello all,
> Thanks for including the MAT implementation into aroma - works very
> nicely.
> I have a quick and probably
Hi.
On Mon, Aug 24, 2009 at 12:21 PM, mbaudis wrote:
>
> Dear all,
>
> I have posted a script and associated files to make it easier to:
>
> 1. process various types of Affymetrix genotyping array batches, using
> aroma.affymetrix, but with
>
> 2. (IMHO) improved value & segmentation plotting opt
Hi.
On Thu, Aug 20, 2009 at 11:25 PM, ssv wrote:
>
> Hi Henrik
>
> I was benchmarking aroma.affymetrix performance on 72 affymetrix 250k
> sty files (36 normal, 36 tumor- paired analysis). Here is what I have
> so far:
>
> ==
> 1) setting up CEL sets and locating t
Hi.
On Fri, Aug 21, 2009 at 12:51 AM, gunes gundem wrote:
> Hi all,
> I installed aroma.affymetrix a couple of days ago and wanted to try a paired
> analysis with a very small data set: 2 cancerous samples and the 2
> corresponding normals. I followed the vignette for 5.0/6.0.
FYI: It looks like
Hi Henrik
Thanks for the reply. Script I am following is as follows:
=
library(aroma.affymetrix);
log <- Arguments$getVerbose(-4, timestamp=TRUE);
dataSetName <- "adeno_carcinoma";
chipTypes <- c("Mapping250K_Sty");
#---
I forgot to add that cel files were (paired, 250k ) 74.
--~--~-~--~~~---~--~~
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete co
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