[BioC] MethyLumiM to MethyLumiSet?
Victoria Svinti
victoria.svinti at igmm.ed.ac.uk
Thu Apr 3 17:05:41 CEST 2014
Hi Tim
I don’t know why this coercion is still not working for me. I thought you had implemented it earlier in this thread.
Error in as(lumiM, "MethyLumiSet") : no method or default for coercing “MethyLumiM” to “MethyLumiSet”
Would you know why ? (tried on both mac os and unix cluster (R.3.0.0))
Thanks
Vicky
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] tools parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] lumi_2.13.6 BiocInstaller_1.12.0 methylumi_2.8.0 matrixStats_0.8.12
[5] ggplot2_0.9.3.1 reshape2_1.2.2 Biobase_2.21.7 BiocGenerics_0.8.0
[9] scales_0.2.3
loaded via a namespace (and not attached):
[1] affy_1.39.2 affyio_1.29.3 annotate_1.39.0 AnnotationDbi_1.24.0
[5] base64_1.1 beanplot_1.1 Biostrings_2.29.19 bumphunter_1.1.17
[9] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0
[13] digest_0.6.3 doRNG_1.5.5 foreach_1.4.1 GenomicRanges_1.13.45
[17] grid_3.0.2 gtable_0.1.2 illuminaio_0.3.10 IRanges_1.19.38
[21] iterators_1.0.6 itertools_0.1-1 KernSmooth_2.23-10 labeling_0.2
[25] lattice_0.20-24 limma_3.17.24 locfit_1.5-9.1 MASS_7.3-29
[29] Matrix_1.1-0 mclust_4.2 mgcv_1.7-27 minfi_1.7.15
[33] multtest_2.17.0 munsell_0.4.2 nleqslv_2.0 nlme_3.1-111
[37] nor1mix_1.1-4 pkgmaker_0.17.4 plyr_1.8 preprocessCore_1.23.0
[41] proto_0.3-10 R.methodsS3_1.5.2 RColorBrewer_1.0-5 registry_0.2
[45] reshape_0.8.4 rngtools_1.2.3 RSQLite_0.11.4 siggenes_1.35.0
[49] splines_3.0.2 stats4_3.0.2 stringr_0.6.2 survival_2.37-4
[53] XML_3.95-0.2 xtable_1.7-1 XVector_0.1.4 zlibbioc_1.7.0
--
Victoria Svinti
Colon Cancer Genetics Group
MRC Human Genetics Unit, IGMM
University of Edinburgh, Western General Hospital,
Crewe Road, Edinburgh, EH4 2XU
On 7 Nov 2013, at 15:06, Allegra A. Petti <apetti at genome.wustl.edu> wrote:
> Hi Tim,
>
> Thanks - this all seems extremely useful, especially the titrated mixture samples. I was thinking of generating some such (partially artificial) data sets myself, but it's great if they already exist!
>
> Allegra
>
> On Nov 6, 2013, at 6:28 PM, "Tim Triche, Jr." <tim.triche at gmail.com> wrote:
>
>> 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/inst/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
>>
>>
>> On Wed, Nov 6, 2013 at 10:25 AM, Allegra A. Petti <apetti at 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 at 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 at 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 at 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
>>>>>
>>>>>
>>>>> On Sun, Nov 3, 2013 at 8:26 AM, Martin Rijlaarsdam <m.a.rijlaarsdam at 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 at 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 at 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
>>>>>
>>>>>
>>>>> On Fri, Nov 1, 2013 at 1:32 AM, Martin Rijlaarsdam <m.a.rijlaarsdam at 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 at 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 at 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
>>>>> >
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>>>>
>>>>
>>>> ____ 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.
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>>
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>
>
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