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

[James W. MacDonald]

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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>>     Scotland, with registration number SC005336.
>>
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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