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/inst/buildScripts/?root=aroma-dots
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.
>
>
> You received this message because you are subscribed to the Google Groups
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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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