Thank you.
On Dec 4, 5:58 pm, Henrik Bengtsson
wrote:
> Hi.
>
>
>
>
>
> On Fri, Dec 4, 2009 at 2:48 PM, zaid wrote:
> > Hello Henrik,
>
> > print(cdf)
> > AffymetrixCdfFile:
> > Path: annotationData/chipTypes/HuEx-1_0-st-v2
> > Filename: HuEx-1_0-st-v2.cdf
> > Filesize: 933.84MB
> > Chip type: H
Hi.
On Fri, Dec 4, 2009 at 2:48 PM, zaid wrote:
> Hello Henrik,
>
> print(cdf)
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/HuEx-1_0-st-v2
> Filename: HuEx-1_0-st-v2.cdf
> Filesize: 933.84MB
> Chip type: HuEx-1_0-st-v2
> RAM: 0.00MB
> File format: v3 (text; ASCII)
> Dimension: 2560x2560
Hello Henrik,
print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/HuEx-1_0-st-v2
Filename: HuEx-1_0-st-v2.cdf
Filesize: 933.84MB
Chip type: HuEx-1_0-st-v2
RAM: 0.00MB
File format: v3 (text; ASCII)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 1432154
Cells per unit: 4.58
Hi,
Q1. What does print(cdf) on that CDF below report? By default you get
an exception if you try to use an ASCII CDF.
Q2. What is your sessionInfo()?
/Henrik
On Fri, Dec 4, 2009 at 2:10 PM, zaid wrote:
> Hi Mark,
>
> Actually the run took about 14 hours.
>
> I thought I was using a binary CD
Hi Mark,
Actually the run took about 14 hours.
I thought I was using a binary CDF file but it seems the one I used is
ASCII. (shouldnt the program warn me if Im not uisng binary?)
They are on local disk and we want to do probeset-only. (FYI the
folder that contains the raw data is 2.33 GB in siz
Hi Zaid.
As I mentioned before, I'd be careful with fitting models on
unnormalized data, but I'll assume you know what you are doing.
Definitely no need to run things in smaller chunks. aroma.affymetrix
does this already to save on memory. The first time through may take
a bit longer, but
Hello Mark,
Thank you for your help.
I'm running the aroma.affymetrix package in R with no normalization as
you have outlined.
I'm using 38 cel files and running a windows vista 64 bit edition on a
quad core intel core 2 processor with 8 gigs of RAM.
the last two steps of "plmTr <- ExonRmaPlm(cs
Hi Elai/Zaid.
You'll want to be careful with all this (i.e. linear models on
unnormalized data ... or maybe you are standardizing some other way),
but yes you can run the probe level model fits on any AffymetrixCelSet
object.
The standard RMA procedure would BG adjust, then quantile normali
Henrik
Is it possible to use aroma to run an RMA implementation without
quantile normalization? Zaid- have you tried this?
Best,
Elai
CSO
GenomeDx Biosciences
On Nov 28, 5:51 am, Henrik Bengtsson wrote:
> Hi Zaid,
>
> I think you have mistaken the aroma.affymetrix mailing list as being a
> mailin
