Update,
I've updated affxparser so these warnings are no longer generated.
When affxparser v1.15.4 becomes available on BioC devel, you can
install it and these warnings will also go away.
/Henrik
On Tue, Feb 10, 2009 at 8:08 PM, Henrik Bengtsson
wrote:
> Hi,
>
> first of all, these warnings
Hi,
first of all, these warnings are ok and have no effect. There is no
need to convert your CEL files. The warnings only occur with CEL
files of the most recent Affymetrix Command Console (aka Calvin) file
format. If you do:
cf <- getFile(cstest, 1);
print(cf);
you will see that the CEL fil
Hi.
On Tue, Feb 3, 2009 at 10:39 PM, David Rosenberg
wrote:
>
> Thank you greatly for your help. A couple of additional questions:
[snip]
> 2.) I don't fully follow the acc model described in the CRMA paper
> (2008). The section in question references a 2001 Wirapati P, Speed
> T. paper
Hi.
On Tue, Feb 3, 2009 at 10:39 PM, David Rosenberg
wrote:
>
> Thank you greatly for your help. A couple of additional questions:
> 1.) With the affxparser writeCdfx functions, it looks as though
> you are directly writing the binary data of correct endianness rather
> than inlining/sw
This is where i ran the above code:
aroma.affymetrix v1.0.0 (2009-01-12)
R version 2.8.0 (2008-10-20)
the CDFs are downloaded from
http://groups.google.com/group/aroma-affymetrix/web/hs-prompr-v02-human-promoter-tiling-1-0r
On Feb 11, 12:37 pm, Jason Li wrote:
> Why do i get all these warnings
Why do i get all these warnings when "printing" binary CEL files?
(Human promoter array)
After i converted the files into text format using Affymetrix Power
Tools, then there is no more warnings. But i thought binary files are
supported?
Thanks
Jason Li
> library(aroma.affymetrix)
> verbose <-
Hi,
I have come across some missing probes in the mogene10st.db package. I
am analysing my data using the aroma package and have included some of
my code:
ces = getChipEffectSet(plm)
gExprs = extractDataFrame(ces, units=NULL, addNames=TRUE)
affyIDs = gExprs$unitName
affyIDs[which(affyIDs %in%
Hi,
since there are different number of tumors and normals I assume these
are not paired in any sense. To use the robust average of the 33
normal samples as the reference (for each of the 141 tumors), do:
ceNN <- getAverageFile(cesNN, verbose=log);
glad <- GladModel(cesNT,ceNN); # Not cesNN
/
Hi Henrik,
Thank you for you reply, I have 141 tumor test samples, and 33
normal samples, and I want to use
the 33 normal samples as the reference set, when I try GladModel or
CbsModel, I got the error message:
> glad <- GladModel(cesNT,cesNN)
Loading required package: GLAD
[1] "Have fu
Hi Henrik,
Indeed the files were corrupted, re-downloading them did the trick.
Thanks a lot,
Armand
On Tue, Feb 10, 2009 at 7:45 PM, Henrik Bengtsson wrote:
>
> Hi.
>
> On Tue, Feb 10, 2009 at 10:34 AM, Armand Valsesia
> wrote:
> >
> > Dear Henrik,
> >
> > I am trying to analyse some Affy6 data
Hi.
On Tue, Feb 10, 2009 at 10:34 AM, Armand Valsesia
wrote:
>
> Dear Henrik,
>
> I am trying to analyse some Affy6 data, but I am stuck at reading the
> ugp file.
> For some reasons, I got "Exception: Failed to retrieve genome
> information for this chip type: GenomeWideSNP_6"
> (cf code and se
Dear Henrik,
I am trying to analyse some Affy6 data, but I am stuck at reading the
ugp file.
For some reasons, I got "Exception: Failed to retrieve genome
information for this chip type: GenomeWideSNP_6"
(cf code and sessionInfo below).
The files under annotationData/chipTypes/GenomeWideSNP_6
Hi Simon.
See comments below.
> I am using the mouse gene ST arrays and am having problems with
> annotation. When i write a csv file, the annotation is only the
> probeset_id, no gene names or accession numbers etc.
That's what it should be. Actually, its the 'transcript_cluster_id'.
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