Thank you!!
On 10月23日, 上午1时55分, Henrik Bengtsson wrote:
> Hi
>
> On Fri, Oct 21, 2011 at 8:17 PM, marco wrote:
> > Thanks a lot!!
> > Yes,i did the same job previously.
> > How does aroma.affymetrix make the result "persistent" and
> > "memorize
gt; On Fri, Oct 21, 2011 at 8:15 AM, marco wrote:
> > Hello Henrik and everyone else
> > I currently run RMA in aroma.affymetrix on dataset GSE21034 which
> > contains 179 human exon 1.0 ST arrays. i use a custom CDF,
> > huex10stv2hsrefseqcdt, from brainarray. the resulti
Hello Henrik and everyone else
I currently run RMA in aroma.affymetrix on dataset GSE21034 which
contains 179 human exon 1.0 ST arrays. i use a custom CDF,
huex10stv2hsrefseqcdt, from brainarray. the resulting data matrix
contains 42667 rows.What supprised me is the whole processing finished
in
Hello every one!!
Is there any way in aroma.affymetrix to measure how well a gene is
detected for human exon 1.0 ST array and human Gene 1.0 ST array? ( I
mean method of same or similar function with paCalls() in package
oligo)
Thanks a lot!
--
When reporting problems on aroma.affymetrix, mak
Dear Madam or Sir
Is there any way in aroma.affymetrix for measuring how well a gene
is detected for human exon 1.0 ST array and human Gene 1.0 ST array? I
mean method with same function as paCalls() in package oligo.
Thanks a lot!!
--
Lin Pei
graduate student
Cancer Institute
Southern Medi
ompared to "fit"?
Best Regards
Marco
--
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 code example.
You received this message because you ar
CbsModel(cesA,c(sc264,sc368))
Thanks for the help!
Best Regards
Marco
R version 2.9.0 (2009-04-17)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;L
Dear Henrik,
I have a problem when I process my 6.0 arrays to extract CNV with CBS
(CRMA v2). Unfortunatly, seems very hard to understand my self what is
wrong from the error message. Do you have any idea?
##
cbs <- CbsModel(cesN)
cnrs <- getRegions(cbs, verbose=verbose
aroma is the allele B of affy. Is
that the case ?
thanks a lot for the help!
Best Regards
Marco
On Sep 16, 6:56 am, Pierre Neuvial wrote:
> Hi Marco,
>
> In case you haven't solved your problem yet...
>
> I think they should be the same if you have analyzed your data us
uencies estimated by pooling a ctrl cohort but it seems
to me that the two "B" do not correspond to each other. Is there any
way to correspond the alleles?
Best Regards
Marco
--~--~-~--~~~---~--~~
When reporting problems on aroma.affymetrix, make sure 1) to
ts.
3. Is there a way to upload figures on this group? I have done some
diagnositc plots that might be interesting for other users.
Best Regards
Marco
On 26 Juni, 07:35, Henrik Bengtsson wrote:
> Hi.
>
> 2009/6/24 marco :
>
>
>
> > Dear Henrik,
>
> > I
Dear Henrik,
I wonder if aroma.affymetrix is suitable for pooled GWA studies and
if you have any experience with this subject. In principle this
consists in extracting the RAS scores, so should be doable. I have the
following specific questions and snippet:
1. by using :
plm <- AvgCnPlm(csN,
ings, do:
>
> cesR1 <- newInstance(ces1, files=list(ceR1));
> cbs <- CbsModel(ceR1, ceR2);
>
> Does this work?
>
> /H
>
> On Tue, Jun 9, 2009 at 12:03 PM, marco wrote:
>
> > Henrik
>
> > seems like it does not work. I went on to R2.9.0 with lat
Henrik
seems like it does not work. I went on to R2.9.0 with latest version
of aroma but I get the following:
I tried also the getAverageFile() function but with the same result. I
guess the two functions do the same thing or a very similar one?
Marco
cdf <- AffymetrixCdfFile$byChipT
quality of the arrays play a role? The QC figures are quite
bad.
Best Regards
Marco
##
> cesN <- process(fln, verbose=verbose)
20090609 15:57:45|Normalizing set for PCR fragment-length effects...
20090609 15:57:45| Ident
<- CbsModel(ces1,ces2)
ce <- ChromosomeExplorer(cbs)
print(ce)
process(ce, chromosomes=c(1:23), verbose=verbose)
Best Regards
Marco
--~--~-~--~~~---~--~~
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the pack
Henrik,
do you have any idea how long it will take to check it out?
Cheers
Marco
On 28 Okt, 23:16, "Henrik Bengtsson" <[EMAIL PROTECTED]> wrote:
> Hi.
>
> On Tue, Oct 28, 2008 at 3:13 AM, marco <[EMAIL PROTECTED]> wrote:
>
> > Dear Henrik,
>
&
lorer(cbs)
print(ce)
process(ce,arrays=c(21:26), chromosomes=c(1:23), verbose=verbose)
### for non sex corrected
cbs <- CbsModel(cesN) #This calculates CNVs with reference the
robust median estimate from mall the arrays
print(cbs)
ce <- ChromosomeExplorer(cbs)
print(ce)
pro
Dear Henrik,
the trick is to have an empty line between each array in the saf
file!
This would work!
#
name:MD10
tags:XY
name:MD11
tags:XY
name:MD12
tags:XY
name:MD13
...
...
Cheers
Marco
On Oct 9, 11:15 pm, "Henrik Bengtsson" <[EMAIL PROTECTED]> wrote:
> Hi.
>
Dear Henrik,
seem that the file is found, but I still have the same problem. I
wonder if the format might be confusing for the software?
Actually the important thing is that the arrays are processed with the
right number of X/Y chromosomes.
Is there any other way to check it?
Cheers
Marco
digest_0.3.1
matrixStats_0.1.3
[10] R.rsp_0.3.4 R.cache_0.1.7
R.utils_1.0.4
[13] R.oo_1.4.6 R.methodsS3_1.0.3
Best Regards
Marco
On Sep 19, 10:10 pm, "Henrik Bengtsson" <[EMAIL PROTECTED]>
wrote:
> Hi.
>
> On Fri, Sep 19, 2008 at 4:35 AM, mar
for reference
Is these possible in aroma.affymetrix?
I tried
test <-extract(cesN,c(21:26))
reference <- extract(cesN,c(1:20))
cbs <- CbsModel(test,reference)
this of course does not work, since CbsModel expects a paired analysis
here
Is there a workaround ?
Cheers
Mar
?
Regards
Marco
--~--~-~--~~~---~--~~
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 code example.
You received this message
. Would this be
reccomended?
Cheers
Marco
On Aug 29, 8:38 pm, "Henrik Bengtsson" <[EMAIL PROTECTED]> wrote:
> Hi,
>
> On Fri, Aug 29, 2008 at 2:15 AM, mbaudis <[EMAIL PROTECTED]> wrote:
>
> > I can support Henrik's observation regarding the HapMap sample
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