Dear Henrik,
Thank you for this clarification.
Since I am still using an older version of aroma.affymetrix which does
not contain parameter 'lengthRange' I cannot specify the fragment
length range. However, at the moment I do not see any disadvantage in
not specifying lengthRange. When I compare the the CN ranges obtained
with GLAD between na30 and na31 there are only slight differences due
to the different annotations. What is your opinion?
Best regards
Christian
On May 26, 11:01 pm, Henrik Bengtsson <henrik.bengts...@aroma-
project.org> wrote:
> Hi.
>
> On Thu, May 26, 2011 at 4:05 AM, cstratowa
>
> <christian.strat...@vie.boehringer-ingelheim.com> wrote:
> > Dear Henrik,
>
> > Thank you for the update.
>
> > Meanwhile I have already created the ufl/ugp files by simply modifying
> > your R-scripts GenomeWideSNP_6,UFL,na30.R and
> > GenomeWideSNP_6,UGP,na30.R.
>
> > Thus, my question is: Did you do something special or do you still use
> > these R-scripts?
>
> Nope, nothing special, except that I made sure that the file footer
> reflects the fact that the date and my initials are correct.
>
> One more thing specific to the na30 -> na31 transition: Affymetrix no
> longer filter the PCR fragment-length data, which means that the new
> UFL files now contains fragment lengths of a large range. You now
> have to specify the range as FragmentLengthNormalization(...,
> lengthRange=c(400,2000)).
>
>
>
> > BTW, on your new web-site I can no longer find these scripts. Are they
> > still available?
>
> Yes, I did remove the links from the website because it is too much
> work to also keep those links up-to-date with everything else.
> Instead, I have added the archive of all build scripts (sorted by chip
> type and NA revision) to the package itself so that they will be
> accessible via:
>
> path <- system.file("buildScripts/", package="aroma.affymetrix");
>
> This will be available in the next release of aroma.affymetrix. Until
> then, you can also grab/browse them via:
>
> https://r-forge.r-project.org/scm/viewvc.php/pkg/aroma.affymetrix/ins...
>
> As you'll see, that for GenomeWideSNP_6 I am moving towards setting up
> somewhat interactive user scripts for doing this. You may have to
> install the R.menu package, i.e.
>
> source("http://aroma-project.org/hbLite.R";);
> hbLite("R.menu");
>
> Hope this helps
>
> Henrik
>
>
>
> > Best regards
> > Christian
>
> > On May 26, 3:36 am, Henrik Bengtsson <henrik.bengts...@aroma-
> > project.org> wrote:
> >> A late follow up/to close this thread:
>
> >> The requested na31/hg19 annotation files are now available:
>
> >>http://aroma-project.org/chipTypes/GenomeWideSNP_6
>
> >> /Henrik
>
> >> On Mon, Mar 28, 2011 at 6:48 AM, cstratowa
>
> >> <christian.strat...@vie.boehringer-ingelheim.com> wrote:
> >> > Dear Henrik,
>
> >> > I am also looking for the new (old) na31 annotation files for SNP6.
>
> >> > I have seen that for the Nsp/Sty arrays you have put the na31 (hg19)
> >> > ufl/ugp files on the Chip types web-site for download.
>
> >> > However, the web-site for SNP6 still contains the old na30 (hg18) ufl/
> >> > ugp files.
> >> > Is it possible to update this site to the new na31 (hg19) ufl/ugp
> >> > files, too?
>
> >> > Best regards
> >> > Christian
>
> >> > On Feb 2, 9:39 am, Mete Civelek <mete.cive...@gmail.com> wrote:
> >> >> Hi All,
>
> >> >> A few weeks ago there was a discussion about ugp and ufl files based
> >> >> on the hg19 annotation. Are those files available for share?
>
> >> >> Thank you
>
> >> > --
> >> > 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.
>
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>
> > --
> > 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.
>
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--
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.
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