re ok).
PS2. I'll try to update the package so it gives a more informative
error message early on if RColorBrewer is missing.
On Wed, Jul 1, 2009 at 2:32 AM, Myriam Peyrard wrote:
>
> Dear Henrik,
>
> I deleted reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/ and all its
> s
Dear Henrik,
I deleted reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/ and all its
subdirectories. Then did: process(ce, arrays=1, chromosomes=19, verbose=-20)
and here is the entire output:
Generating ChromosomeExplorer report...
Setting up ChromosomeExplorer report files...
Copying template fi
extractMatrix(ceR, drop=TRUE)
str(thetaR)
num [1:1881415] 4448 1674 6573 9634 776 ...
print(summary(thetaR))
Min. 1st Qu. Median Mean 3rd Qu.Max.
-1493192488855097158 72180
print(summary(is.finite(thetaR)))
ModeTRUENA's
logical 1881415 0
Do
open them "manually"? What internet browser
do you use?
/Henrik
On Mon, Jun 29, 2009 at 12:50 AM, Myriam Peyrard
wrote:
> Thank you Henrik.
> I re-run the whole until fragment normalization in the script I sent you
> before (see below).
> Then did:
> plotDensity(cesN)
&
(Myriam)
To: aroma-affymetrix
>
> Before I or someone else try to tackle this, what does sessionInfo()
> report when you run your script. /H
>
> 2009/6/22 Myriam Peyrard :
> >
> > Dear Henrik,
> >
> > I do not get any result, on any chromosomes. But I get all
From: aroma-affymetrix@googlegroups.com
[mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
Sent: den 18 juni 2009 18:25
To: aroma-affymetrix@googlegroups.com
Subject: Re: No CN estimates for SNP 6.0 (Was: Re: [aroma.affymetrix] Re:
CNV analys 28 st SNP 6.0 arrays)
Hi,
ar
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
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
Ok, thank you so much, Pierre. I shall try and if not working, get back
to you again.
The output I gave you was the one I got but, finally (my second day
using R and Aroma Affymetrix, as I sai, a brand new beginner!!!), at the
end of the day, I realized that I had forgotten to open the aroma
libra
