[BioC] problem with 'FDb.InfiniumMethylation.hg19'

[Victoria Svinti]

Hi Jim,

Thanks for tip re. posting. Good to know that it's safe to use IlluminaHumanMethylation450k.db for now.

Best wishes,
Victoria


On 1 Jul 2013, at 14:53, James W. MacDonald <jmacdon at u.washington.edu> wrote:

> Hi Victoria,
> 
> Please don't take conversations off-list (e.g., use Reply-all, instead of Reply when responding). We like to think of the list archives as a repository of knowledge, so making conversations private defeats that purpose.
> 
> On 6/29/2013 4:11 PM, Victoria Svinti wrote:
>> Hi Jim,
>> 
>> Thank you for your reply. I tried IlluminaHumanMethylation450k.db first, but I get a warning message saying that it is deprecated, and that I should use FDb.InfiniumMethylation.hg19 instead. Should I just ignore that?
> 
> Well, yes. The deprecation message comes from the IlluminaHumanMethylation450k.db package itself, and the package will become defunct at some point in time. And I assume that the lumi and in particular the methylumi packages will be updated in the interim to account for the deprecation of that package.
> 
> But in the interim, you still need the IlluminaHumanMethylation450k.db package if you want to analyze your data using these packages.
> 
> Best,
> 
> Jim
> 
> 
>> 
>> Much appreciated,
>> Vicky
>> 
>> 
>> On 28 Jun 2013, at 21:00, James W. MacDonald <jmacdon at uw.edu <mailto:jmacdon at uw.edu>> wrote:
>> 
>>> Hi Victoria,
>>> 
>>> I think you want the IlluminaHumanMethylation450k.db package rather than the FDb package.
>>> 
>>> Best,
>>> 
>>> Jim
>>> 
>>> On Jun 28, 2013 3:19 PM, "Victoria Svinti" <victoria.svinti at igmm.ed.ac.uk <mailto:victoria.svinti at igmm.ed.ac.uk>> wrote:
>>> 
>>>    Hi there,
>>> 
>>>    I came across another error when trying to load this annotation:
>>> 
>>>    obj <- lumiMethyR(fileName, lib="FDb.InfiniumMethylation.hg19")
>>>    Error in get(paste(sub("\\.db$ <smb://.db$>", "", lib),
>>>    "COLORCHANNEL", sep = "")) :
>>>      object 'FDb.InfiniumMethylation.hg19COLORCHANNEL' not found
>>> 
>>>    Does anyone else have this problem? Also, I still get the
>>>    'condition has length > 1 …' error after downloading
>>>    BSgenome.Hsapiens.UCSC.hg19...
>>> 
>>>    Would appreciate your thoughts.
>>> 
>>>    Thanks,
>>>    Vicky
>>> 
>>>    ----
>>> 
>>>    > sessionInfo()
>>>    R version 3.0.0 (2013-04-03)
>>>    Platform: x86_64-unknown-linux-gnu (64-bit)
>>> 
>>>    locale:
>>>     [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>>>     [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>>>     [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
>>>     [7] LC_PAPER=C                 LC_NAME=C
>>>     [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>>    [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>>> 
>>>    attached base packages:
>>>    [1] parallel  stats     graphics  grDevices utils     datasets
>>>     methods
>>>    [8] base
>>> 
>>>    other attached packages:
>>>     [1] annotate_1.38.0                    BiocInstaller_1.10.2
>>>     [3] FDb.InfiniumMethylation.hg19_1.0.1 rtracklayer_1.20.2
>>>     [5] Biostrings_2.28.0                  GenomicFeatures_1.12.2
>>>     [7] AnnotationDbi_1.22.6               GenomicRanges_1.12.4
>>>     [9] IRanges_1.18.1                     methylumi_2.6.1
>>>    [11] ggplot2_0.9.3.1                    reshape2_1.2.2
>>>    [13] scales_0.2.3                       lumi_2.12.0
>>>    [15] Biobase_2.20.0                     BiocGenerics_0.6.0
>>> 
>>>    loaded via a namespace (and not attached):
>>>     [1] affy_1.38.1                        affyio_1.28.0
>>>     [3] beanplot_1.1                       biomaRt_2.16.0
>>>     [5] bitops_1.0-5                       BSgenome_1.28.0
>>>     [7] BSgenome.Hsapiens.UCSC.hg19_1.3.19 colorspace_1.2-2
>>>     [9] DBI_0.2-7                          dichromat_2.0-0
>>>    [11] digest_0.6.3                       grid_3.0.0
>>>    [13] gtable_0.1.2                       illuminaio_0.2.0
>>>    [15] KernSmooth_2.23-10                 labeling_0.2
>>>    [17] lattice_0.20-15                    limma_3.16.5
>>>    [19] MASS_7.3-26                        Matrix_1.0-12
>>>    [21] matrixStats_0.8.1                  mclust_4.1
>>>    [23] mgcv_1.7-24                        minfi_1.6.0
>>>    [25] multtest_2.16.0                    munsell_0.4
>>>    [27] nleqslv_2.0                        nlme_3.1-109
>>>    [29] nor1mix_1.1-4                      plyr_1.8
>>>    [31] preprocessCore_1.22.0              proto_0.3-10
>>>    [33] RColorBrewer_1.0-5                 RCurl_1.95-4.1
>>>    [35] reshape_0.8.4                      R.methodsS3_1.4.2
>>>    [37] Rsamtools_1.12.3                   RSQLite_0.11.4
>>>    [39] siggenes_1.34.0                    splines_3.0.0
>>>    [41] stats4_3.0.0                       stringr_0.6.2
>>>    [43] survival_2.37-4                    tools_3.0.0
>>>    [45] XML_3.98-1.1                       xtable_1.7-1
>>>    [47] zlibbioc_1.6.0
>>>    >
>>> 
>>> 
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>>> 
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>> 
>> 
>> 
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
> 
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
> 
> 


-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.