[Bioc-devel] is it normal for makeDBPackage to take a> VERY long time?

Tim Triche, Jr. tim.triche at gmail.com
Tue Jan 18 23:14:44 CET 2011

No doubt, I was not suggesting otherwise. My wording was unclear; I had two orthogonal questions that belonged in two separate emails. 

My apologies for the ruckus. 


On Jan 18, 2011, at 2:06 PM, Pan Du <dupan at northwestern.edu> wrote:

> Hi Tim
> I am agree with Sean. At least, we need to have one Bioconductor annotation
> package based on manufacturer provided mapping information. Of course, you
> can add additional tables in the library. Based on my experience, looks like
> Illumina has much improved annotation maintenance now.
> Thanks for your effects!
> Pan
> On 1/18/11 2:40 PM, "bioc-devel-request at r-project.org"
> <bioc-devel-request at r-project.org> wrote:
>> Message: 2
>> Date: Tue, 18 Jan 2011 15:28:23 -0500
>> From: Sean Davis <sdavis2 at mail.nih.gov>
>> To: "Tim Triche, Jr." <ttriche at usc.edu>
>> Cc: "bioc-devel at r-project.org" <bioc-devel at r-project.org>
>> Subject: Re: [Bioc-devel] is it normal for makeDBPackage to take a
>> VERY long time?
>> Message-ID:
>> <AANLkTinzY8XOaFv+N4yAXrP=u6JxpwuCnvMo5sDzvwqO at mail.gmail.com>
>> Content-Type: text/plain
>> On Tue, Jan 18, 2011 at 3:13 PM, Tim Triche, Jr. <ttriche at usc.edu> wrote:
>>> Hi all,
>>> Thanks for all the tips and suggestions!   I have updated the 27k and 450k
>>> methylation annotation packages, and will re-run the packaging script in a
>>> few days to see how much of a difference this makes.  I need to update the
>>> 27k annotations anyways, now that I've added some fields and bimaps for my
>>> own purposes (decoding IDAT files and mapping the probes properly).   But,
>>> I've got working builds of the packages now -- whee.
>>> The new 27k and 450k packages are ready (or at least, everything works -- I
>>> am only just learning how to use RUnit properly so the formal tests have not
>>> yet been updated).  Eventually I would like to automate the merging process
>>> for information from Illumina and that which is included from other sources
>>> (Entrez, UCSC, etc).  What is the accepted way of doing this?  I think I
>>> could handle maintenance of these packages if there's a means to properly
>>> automate the merging of manufacturer-specific and assembly-specific data.
>>> For what it's worth, I tried using CHiPpeakAnno, GenomicRanges, and some
>>> other tools (but mostly the former) to annotate a few probes, and I'm not
>>> 100% certain that I did it right.  Absent strand information, which I find
>>> almost indecipherable from Illumina's "TOP/BOT" vs the usual "+/-"
>>> watson/crick notation, the results suggest that a handful of allegedly
>>> upstream CpG island probes are... not.  The re-annotation results do
>>> correspond fairly closely to the actual assay results, though (Jean-Pierre
>>> Issa wanted to compare some Illumina methylation results with those from the
>>> MCA platform in use at MD Anderson, so I said I would try and figure out why
>>> some Illumina probes seem concordant with the MCA probes and some don't...
>>> the reason, if GRanges is correct, is that some of the Illumina probes don't
>>> seem to map where I expected them to).
>>> What's the best way to do reannotation of a platform for specific features?
>>> It took a long time just to map the accessions on the 450k platform, I'm
>>> not real excited about BLATting everything in sight whenever a string
>>> changes somewhere, if I don't have to.
>> Hi, Tim.
>> I would suggest using the annotations supplied by the manufacturer without
>> modification.  Doing otherwise will very likely be a non-trivial exercise,
>> particularly with regard to documenting what has been done.  Of course, feel
>> free to do that with your own versions (or even separate parallel versions)
>> of the packages, but for those for release on bioconductor, I suggest that
>> sticking to the manufacturer's annotations is the best way to go.  Of
>> course, if you find annotation problems, bring those up with Illumina
>> directly, as they have an interest in maintaining relevant and correct
>> annotations.
>> Sean

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