Hello:
I used PdInfo2Cdf to create my own CDF for Mouse Gene ST 1.0 .
However, when I compared with r3 version available from
aroma.affymetrix, I see a small difference:
from r3 version
AffymetrixCdfFile:
Path: annotationData/chipTypes/MoGene-1_0-st-v1
Filename: MoGene-1_0-st-v1,r3.cdf
to apply to design matrix and
contrast matrix? Or should I for each comparison , do RMA and FIRMA
score for exon arrays only involved in that comparison? Thanks for
your input!
Sabrina
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When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2
, then will I be better off if I just use the m=median(firma
score) for each group and rank the the differences of my contrast
group (m1-m2) and find out the most potential splicing events? I guess
I am a little bit confused. Thanks
Sabrina
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When reporting problems on aroma.affymetrix, make sure 1
that is for gene expression. Is 0.01
also a good guess for this firma score purpose? Or should I use 0.001
or some other values? Thanks!
Sabrina
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When reporting problems on aroma.affymetrix, make sure 1) to run the latest
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different. I wonder what is
the right choice to fit my objective. Thanks
Sabrina
--
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
Hi, Mark:
On Nov 17, 11:46 pm, Mark Robinson mrobin...@wehi.edu.au wrote:
Hi Sabrina.
Comments below.
Hi, Mark:
Thanks for the information. What I worried about using coordinate is
that coordinate changes with assembly, while sequences do not change.
I don't know how many psrs are out
:
Hi folks.
Note that you can download these directly with the R/Bioconductor
package 'rtracklayer'. For example:
library(rtracklayer)
session - browserSession(UCSC)
q1 - ucscTableQuery(session, refGene, GenomicRanges(genome = hg18))
refGene - getTable(q1)
Sabrina: I'm actually
Hi, Mark:
Forgot to ask another question. Back to my original question, is there
an (easy) way to map from partial sequence (i.e. the probeset
sequence) to exon sequence in a batch mode or in R? Thanks!
Sabrina
On Nov 16, 8:10 pm, Mark Robinson mrobin...@wehi.edu.au wrote:
Hi folks.
Note
it is in an exon (ENSEMBL) region , or if it is, how do I get
the entire exon sequence and coordinates? Thanks a lot!
Sabrina
--
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
Hi, Jiang:
Can you give me more detail about UCSC RefGene file? Is there a link
to download? Thanks!
Sabrina
On Nov 15, 11:38 am, camelbbs camel...@gmail.com wrote:
hi,
I think you can get the probeset coordinates from affy exon array
annotation files, and you can get exon coordinates from
Hi, Henrik:
It worked! Thanks
Sabrina
library(aroma.affymetrix)
Loading required package: aroma.core
Loading required package: R.cache
R.cache v0.1.7 (2008-02-27) successfully loaded. See ?R.cache for
help.
Error: package 'R.filesets' 0.5.2 was found, but = 0.5.3 is required
by 'aroma.core
the program before, it worked fine . I am using R2.9.1. Thanks
Sabrina
--~--~-~--~~~---~--~~
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
tell whether they are just background noise? I used
Rmabackgroundcorrection
Thanks
Sabrina
On Sep 2, 6:17 pm, Mark Robinson mrobin...@wehi.edu.au wrote:
Hi Sabrina.
Hmm, that does seem unexpected. I would expect that if there are just
a few probes picked out, it shouldn't change that much
Hi, Mark:
for the Unit_id, does it have to be Ensembl gene ID like ENSMUSG?
Lots of genes do not have ensembl assignment from Affy annotation
file. There are lots of missing annotaions, and I still have not found
any good way to deal with it. Do you have any suggestions?
Thanks
Sabrina
Thanks , Mark!
Can you show me /walk me through how to get a new snp-free CDF ? I
finally got the right version of snp and probe mapping so I am ready
to try it out!
Sabrina
On Jun 6, 3:14 am, Mark Robinson mrobin...@wehi.edu.au wrote:
Hi Sabrina.
Comments below.
On 06/06/2009, at 1:57 AM
all affected exons from analysis, how can I do it? I
never worked with SNP data before, can anyone give me a hint? Thanks a
lot!
Sabrina
--~--~-~--~~~---~--~~
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2
.
Of course, I have no way to check the code, just wondering...
On Jan 28, 10:12 pm, Mark Robinson mrobin...@wehi.edu.au wrote:
Hi Sabrina.
First of all, you are somewhat in unchartered waters here. I
personally don't recommend using the 'full' CDF for FIRMA analysis.
Others can disagree
? Thanks!!!
Sabrina
--~--~-~--~~~---~--~~
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
files so you are the right person to ask :)
The code I generated the # of probes per exon is:
nProbesPerExon-readCdfNbrOfCellsPerUnitGroup(getPathname(cdf))
nProbesPerExonVector-unlist(nProbesPerExon)
Thanks and Have a great weekend
Sabrina
On Jan 22, 5:18 pm, Mark Robinson mrobin...@wehi.edu.au
values. I
wonder where went wrong, perhaps fit(firma) step?
Thanks!
Sabrina
On Jan 20, 7:48 pm, Mark Robinson mrobin...@wehi.edu.au wrote:
Hi Sabrina.
Do you have biological replicates of some samples and technical
replicates of others? Or, just technical replicates of everything?
My
for these two
arrays (say sample 1),will it estimate different probe affinity? If it
does , then these chipEffects (gene signals to estimate FIRMA score)
won't be compatible , am I correct? Thanks!
Sabrina
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When reporting problems
) .Or any suggestions about how to
deal with this situation? My goal is to find novel splicing events,
but right now I am just using core annotation to try it out. Thanks!
Sabrina
--~--~-~--~~~---~--~~
When reporting problems on aroma.affymetrix, make sure 1) to run
color coding for these samples on the same graph? Thanks!
Sabrina
On Dec 9, 5:02 pm, Mark Robinson [EMAIL PROTECTED] wrote:
Hi Sabrina.
Great work! See below.
On 10/12/2008, at 5:27 AM, sabrina wrote:
Hi, Mark!
Thank you so much! I think I pretty much figured out how to get
of the annotation file, so some of them I
can't not search. Is there any easy way to do it in R and display it
in R? I usually use Matlab, so I am very unfamiliar with R.
Thank you so much!
Sabrina
--~--~-~--~~~---~--~~
When reporting problems on aroma.affymetrix, make sure 1
the first ID,
it is in Affy annotation file. Can you point out what I did
incorrectly? Thanks !
Sabrina
On Dec 3, 4:53 pm, Mark Robinson [EMAIL PROTECTED] wrote:
Sabrina.
See below.
On 04/12/2008, at 8:41 AM, sabrina wrote:
Hi, Mark:
Thank you so much for the detailed explanation!
Actually
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