Hi all,
the vignette for the somewhat-recent additions in terms of coercion
to/from
lumi and minfi data structures, with notes on bog-standard TCGA data
processing and Ranges-based querying, seems to have built successfully
overnight:
http://www.bioconductor.org/packages/2.14/bioc/vignettes/methylumi/ins
t/doc/methylumi450k.pdf
I shall backport the appropriate bits to the 2.8.x (release) series
and
perhaps expand upon the vignette a little bit. The
preprocessQuantile()
and estimateCellCounts() functions in minfi are great, but they make
certain assumptions that not all users will necessarily feel are
satisfied.
So the less sexy, older pipeline of
methylumi.bgcorr+normalizeMethyLumiSet+BMIQ might be of interest to
some
users. Given that it's trivial to pass off the data to ChAMP for BMIQ
and
genomic mapping, I may as well support that too.
Finally, I've been meaning to upload some titrated mixture samples
that can
serve as artificial "standards" for preprocessing benchmarks, similar
to
the replicates and between/within comparisons that are typical for the
purpose. Since I seem to be too lazy to get them up on GEO, I guess
it's
time for an experimentData package, to be followed at some point be a
proper GEO upload. So I'll get that knocked out as well. (The
samples
have been circulating for a while informally but should be more
broadly
visible, IMHO)
Thanks to everyone who filed bugs or otherwise pushed this along.
--t
*He that would live in peace and at ease, *
*Must not speak all he knows, nor judge all he sees.*
Benjamin Franklin, Poor Richard's
Almanack<http: archive.org="" details="" poorrichardsalma00franrich="">
On Wed, Nov 6, 2013 at 10:25 AM, Allegra A. Petti
<apetti@genome.wustl.edu>wrote:
> Thank you - that would be great. I could not find version 2.9.5
(although
> I did find development version 2.9.1.)
>
> Best,
> Allegra
>
> On Nov 6, 2013, at 11:53 AM, "Tim Triche, Jr."
<tim.triche@gmail.com>
> wrote:
>
> 2.9.5 and later (devel) have the new functionality; I need to
backport it
> to the release version (2.8.x). Thanks for reminding me to do this.
>
> There's also a new vignette in the 2.9.x series which covers all the
> functionality and serves as a unit test.
>
> --t
>
> On Nov 6, 2013, at 8:43 AM, "Allegra A. Petti"
<apetti@genome.wustl.edu>
> wrote:
>
> Hi Tim,
>
> Thank you again for adding the requested function. I was wondering
what
> version of methylumi contains the new function (2.8.1?). Also, is
the
> function analogous to the other conversion function (i.e.
> "as(MethyLumiMdataset,'MethyLumiSet')") or does it have a specific
name?
>
> Best,
> Allegra
>
> On Nov 4, 2013, at 2:19 PM, "Tim Triche, Jr." <tim.triche@gmail.com>
> wrote:
>
> Hi all,
>
> I just committed the changes to the development version of
'methylumi' and
> added a vignette on 450k preprocessing. The changes should
propagate
> overnight and I will backport them to BioC-2.13 as soon as possible.
>
> It should be noted that some conversions are "lossy" -- lumiMethyR
and
> lumIDAT result in loss of out-of-band data from the IDATs, but that
can't
> really be avoided. It does preclude use of the resulting objects as
> RGChannelSets.
>
> The new vignette is rather uncreatively titled methylumi450k.Rnw,
but it
> serves as something of a unit test for all the import,
preprocessing, and
> coercion steps. It also throws a warning when I
> load IlluminaHumanMethylation450k.db, so now I'm going to have to
finally
> address that... time to dogfood the change. It is a bit of a beast
but it
> does give the package a proper workout. I have been seeing some
curious
> issues with methylumi450k.tex disappearing when I run R CMD Sweave
on it,
> so there may be additional checkins to stabilize that.
>
>
>
>
> *He that would live in peace and at ease, *
> *Must not speak all he knows, nor judge all he sees.*
>
> Benjamin Franklin, Poor Richard's
Almanack<http: archive.org="" details="" poorrichardsalma00franrich="">
>
>
> On Sun, Nov 3, 2013 at 8:26 AM, Martin Rijlaarsdam <
> m.a.rijlaarsdam@gmail.com> wrote:
>
>> sorry, forgot to cc the list.
>>
>> Dear Tim,
>>
>> Thanks a lot for the effort! I will most certainly be using it when
it
>> becomes available. I first use some of GenomeStudios normalization
options
>> before exporting the results and importing using lumi, so I cannot
use the
>> IDAT files themselves.
>>
>> Kind regards,
>> Martin
>>
>> --
>> M.A. (Martin) Rijlaarsdam MSc. MD
>> Erasmus MC - University Medical Center Rotterdam
>> Department of Pathology
>> Room Be-432b
>> Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
>> Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The
Netherlands
>>
>> Email: m.a.rijlaarsdam@gmail.com
>> Mobile: +31 6 45408508
>> Telephone (work): +31 10 7033409
>> Fax +31 10 7044365
>> Website:
http://www.martinrijlaarsdam.nl
>>
>>
>> On Fri, Nov 1, 2013 at 5:17 PM, Tim Triche, Jr.
<tim.triche@gmail.com>wrote:
>>
>>> I'll write something and put it into methylumi. The coercion
should not
>>> be terribly difficult, and I need to add more documentation
anyways.
>>>
>>> For the record, there are coercions to and from Minfi data
structures in
>>> methylumi (e.g. as(mset, 'RGChannelSet')) although they depend
upon
>>> information that can only be extracted from the raw IDAT files.
>>>
>>> I don't see this as a bad thing; the practice of keeping raw CEL
files
>>> around from Affy chips led to things like FRMA and SCAN/UPC years
later. I
>>> will be *stoked* when someone comes up with FRMA-for-Illumina and
we can
>>> dispense with batch processing; a recent run with minfi confirmed
that, on
>>> a machine with 64GB of RAM, ~1000 samples choked minfi just like
it did
>>> methylumi. Plus, the probe-specific characteristics of the
platform should
>>> soon be estimable. Cross your fingers and/or watch out for a neat
methods
>>> paper :-)
>>>
>>>
>>>
>>> *He that would live in peace and at ease, *
>>> *Must not speak all he knows, nor judge all he sees.*
>>>
>>> Benjamin Franklin, Poor Richard's
Almanack<http: archive.org="" details="" poorrichardsalma00franrich="">
>>>
>>>
>>> On Fri, Nov 1, 2013 at 1:32 AM, Martin Rijlaarsdam <
>>> m.a.rijlaarsdam@gmail.com> wrote:
>>>
>>>> Dear all,
>>>>
>>>> I have been searching for this for a while as well (also required
to
>>>> combine lumi with minfi & IMA). I have not found a solution so
far. It
>>>> would really help the integrated use of the various available
packages
>>>> if
>>>> this were possible. Any suggestion would be very welcome!
>>>>
>>>> Kind regards,
>>>> Martin
>>>>
>>>>
>>>> --
>>>> M.A. (Martin) Rijlaarsdam MSc. MD
>>>> Erasmus MC - University Medical Center Rotterdam
>>>> Department of Pathology
>>>> Room Be-432b
>>>> Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The
Netherlands
>>>> Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The
>>>> Netherlands
>>>>
>>>> Email: m.a.rijlaarsdam@gmail.com
>>>> Mobile: +31 6 45408508
>>>> Telephone (work): +31 10 7033409
>>>> Fax +31 10 7044365
>>>> Website:
http://www.martinrijlaarsdam.nl
>>>>
>>>>
>>>> On Thu, Oct 31, 2013 at 4:57 PM, Allegra Petti
<apetti@genome.wustl.edu>>>> >wrote:
>>>>
>>>> > Hello,
>>>> >
>>>> > I am analyzing Illumina 450k methylation data using a
combination of
>>>> > functions from multiple R packages, including lumi, methylumi,
and
>>>> > wateRmelon. Although I have found a function to convert a
MethyLumiSet
>>>> > object to a MethyLumiM object, I cannot figure out how to
perform the
>>>> > opposite conversion (from MethyLumiM to MethyLumiSet). I am
>>>> relatively new
>>>> > to R, and would appreciate any advice.
>>>> >
>>>> > Thanks very much,
>>>> > Allegra
>>>> >
>>>> > ____
>>>> > This email message is a private communication. The information
>>>> > transmitted, including attachments, is intended only for the
person or
>>>> > entity to which it is addressed and may contain confidential,
>>>> privileged,
>>>> > and/or proprietary material. Any review, duplication,
retransmission,
>>>> > distribution, or other use of, or taking of any action in
reliance
>>>> upon,
>>>> > this information by persons or entities other than the intended
>>>> recipient
>>>> > is unauthorized by the sender and is prohibited. If you have
received
>>>> this
>>>> > message in error, please contact the sender immediately by
return
>>>> email and
>>>> > delete the original message from all computer systems. Thank
you.
>>>> >
>>>> > ______________________________**_________________
>>>> > Bioconductor mailing list
>>>> > Bioconductor@r-project.org
>>>> >
https://stat.ethz.ch/mailman/**listinfo/bioconductor<
>>>>
https://stat.ethz.ch/mailman/listinfo/bioconductor>
>>>> > Search the archives:
http://news.gmane.org/gmane.**
>>>> > science.biology.informatics.**conductor<
>>>>
http://news.gmane.org/gmane.science.biology.informatics.conductor>
>>>> >
>>>>
>>>> [[alternative HTML version deleted]]
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor@r-project.org
>>>>
https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives:
>>>>
http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>
>>>
>>>
>>
>
>
> ____ This email message is a private communication. The information
> transmitted, including attachments, is intended only for the person
or
> entity to which it is addressed and may contain confidential,
privileged,
> and/or proprietary material. Any review, duplication,
retransmission,
> distribution, or other use of, or taking of any action in reliance
upon,
> this information by persons or entities other than the intended
recipient
> is unauthorized by the sender and is prohibited. If you have
received this
> message in error, please contact the sender immediately by return
email and
> delete the original message from all computer systems. Thank you.
>
>
>
> ____ This email message is a private communication. The information
> transmitted, including attachments, is intended only for the person
or
> entity to which it is addressed and may contain confidential,
privileged,
> and/or proprietary material. Any review, duplication,
retransmission,
> distribution, or other use of, or taking of any action in reliance
upon,
> this information by persons or entities other than the intended
recipient
> is unauthorized by the sender and is prohibited. If you have
received this
> message in error, please contact the sender immediately by return
email and
> delete the original message from all computer systems. Thank you.
>
[[alternative HTML version deleted]]
Hello Tim,
I know this thread was posted all a while ago, but I am working with a methylation dataset now and am encountering similar problems. I am relatively new to all this, but would appreciate any help.
Specifically, when I used your coercion function to convert back to a MethyLumiSet after performing some other functions on my data as a MethyLumiM object, I could no longer subset my MethyLumiSet object. A reproducible example is provided below. I can't tell where it is dropping columns or where the error is occurring. Any help would be appreciated
Thanks,
Rob Busch, MD