On Thu, Sep 3, 2009 at 1:28 AM, JeromeW wrote:
>
>
>
>> > library("aroma.affymetrix");
>> > pathname <-
>> > "annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full.cdf";
>> > cdf <- AffymetrixCdfFile(pathname);
>
> This works!
> Thank you Henrik.
No, no, that is supposed to be a a workar
> > library("aroma.affymetrix");
> > pathname <-
> > "annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full.cdf";
> > cdf <- AffymetrixCdfFile(pathname);
This works!
Thank you Henrik.
--~--~-~--~~~---~--~~
When reporting problems on aroma.affymetrix, mak
Hi,
I have created a cdf and I am trying to check how its running and I have
have this error.Could anyone help me on this.
This is the code:
>
df<-GenericDataFile("annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2.cdf")
> chipType<-"HG-U133_Plus_2"
> cdf<-AffymetrixCdfFile$findByChipType(chi
On Wed, Sep 2, 2009 at 8:28 AM, JeromeW wrote:
>
> Thank you Henrik for your quick reply.
>
> Here is what I get:
>
>> df <-
>> GenericDataFile("annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full.cdf");
>> df;
> GenericDataFile:
> Name: GenomeWideSNP_6
> Tags: Full
> Full name: GenomeW
Thank you Henrik for your quick reply.
Here is what I get:
> df <-
> GenericDataFile("annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full.cdf");
> df;
GenericDataFile:
Name: GenomeWideSNP_6
Tags: Full
Full name: GenomeWideSNP_6,Full
Pathname: annotationData/chipTypes/GenomeWideSNP_6/
So, if none of the stopifnot() tests complaints, then it might be that
the CDF file might be corrupt or incomplete. Compare with the file
size and checksum that I get:
> library("aroma.affymetrix");
> pathname <-
> "annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full.cdf";
> df <- Gen
(sorry for quoting myself)>
I am more and more puzzled... The "findByChipType" method seems to
correctly detect the cdf file:
AffymetrixCdfFile$findByChipType("GenomeWideSNP_6", tags="Full")
[1] "annotationData/chipTypes/GenomeWideSNP_6/
GenomeWideSNP_6,Full.cdf"
--~--~-~--~~-
Hi all
I reply in this thread because I also have the "could not locate a
file" problem which I cannot solve.
My code:
setwd("/x05/people/m140932/eclipse/workspace/CNV"); # here I set the
working directory
library("aroma.affymetrix");
log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE);
o
I just answered this question at:
http://groups.google.com/group/aroma-affymetrix/web/gene-1-0-st-array-analysis
regards,
Math
McGill Uni
On Mon, Aug 31, 2009 at 7:46 PM, Henrik Bengtsson wrote:
>
> On Thu, Aug 27, 2009 at 10:12 AM, Diya Vaka wrote:
> >
> > Dear Henrik,
> >
> > Thank you for th
On Thu, Aug 27, 2009 at 10:12 AM, Diya Vaka wrote:
>
> Dear Henrik,
>
> Thank you for the help.Now its running fine.
Good.
>
> I want to get the top 100 over expressed genes and under expressed
> genes from this data.
>
> So can I use the affy and limma packages for that or is there any
> thing
Dear Henrik,
Thank you for the help.Now its running fine.
I want to get the top 100 over expressed genes and under expressed
genes from this data.
So can I use the affy and limma packages for that or is there any
thing specifically in aroma.affymetrix.
Thanks in advance,
Diya
On Aug 27, 12:3
Hi.
On Wed, Aug 26, 2009 at 12:10 PM, Diya Vaka wrote:
>
> Hi all,
>
> I am trying to analyze MoGene-1_0-st-v1 data and I these are the
> errors:
>
> In MoGene-1_0-st-v1 directory I have the MoGene-1_0-st-v1.cdf file and
> I ran the following commands
>
> setwd("C:/Documents and Settings/annotati
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