Reading IDAT files from Illumina HumanMethylation450 BeadChip with beadarray
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@mariakeays-8927
Last seen 6.0 years ago
United Kingdom

Hello,

I'm getting the following error when trying to read IDAT files from the Illumina HumanMethylation450 BeadChip:

> library( beadarray )
> idats <- list.files( pattern = "\\.idat$" )
> dataSet <- readIdatFiles( idats )
Error in idatData$Quants[, "CodesBinData"] : subscript out of bounds

Is it possible to read these files with beadarray?

The files I've been using are available here: https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-70737/ and here: https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3161/

Thanks!

Maria

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=C
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
 [7] LC_PAPER=en_GB.UTF-8       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] illuminaio_0.10.0   beadarray_2.18.0    ggplot2_1.0.1
[4] Biobase_2.28.0      BiocGenerics_0.14.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.1          AnnotationDbi_1.30.1 XVector_0.8.0
 [4] magrittr_1.5         GenomicRanges_1.20.8 MASS_7.3-44
 [7] IRanges_2.2.9        munsell_0.4.2        colorspace_1.2-6
[10] stringr_1.0.0        plyr_1.8.3           GenomeInfoDb_1.4.3
[13] tools_3.2.2          base64_1.1           grid_3.2.2
[16] gtable_0.1.2         DBI_0.3.1            digest_0.6.8
[19] reshape2_1.4.1       S4Vectors_0.6.6      RSQLite_1.0.0
[22] limma_3.24.15        stringi_0.5-5        BeadDataPackR_1.20.0
[25] scales_0.3.0         stats4_3.2.2         proto_0.3-10
 
beadarray illumina methylation microarray • 1.2k views
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@sean-davis-490
Last seen 6 weeks ago
United States

I'd suggest using the minfi or RnBeads packages for illumina methylation analysis.

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Ah thanks for the suggestions -- I'll check them out!

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