Question: Reading IDAT files from Illumina HumanMethylation450 BeadChip with beadarray
0
gravatar for maria.keays
3.8 years ago by
United Kingdom
maria.keays0 wrote:

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
 
ADD COMMENTlink modified 3.8 years ago by Sean Davis21k • written 3.8 years ago by maria.keays0
Answer: Reading IDAT files from Illumina HumanMethylation450 BeadChip with beadarray
0
gravatar for Sean Davis
3.8 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:

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

ADD COMMENTlink written 3.8 years ago by Sean Davis21k

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

ADD REPLYlink written 3.8 years ago by maria.keays0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 243 users visited in the last hour