I am still trying to get beadarray's readIllumina() working with recently acquired data from HT-12 v4 beadchips and using a sample sheet. No matter what I was trying in that sample sheet, I always got:
Error in analyseDirectory(dir = x, sectionNames = as.character(dirs[[x]]), : Directory does not exist.
So I started to debug the readIllumina() function and noticed that it is truncating the chip's identifier, in turn looking for the wrong directories.
Apparently Illumina is using longer identifiers since last October which breaks beadarray's handling of samplesheets and in turn prevents reading data!
I can provide sample files for assistance in fixing this issue, please get in touch and I'll send them along.
Thank you very much & greetings from Heidelberg
R version 3.4.0 (2017-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 8 (jessie) Matrix products: default BLAS: /usr/local/lib/R/lib/libRblas.so LAPACK: /usr/local/lib/R/lib/libRlapack.so locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8  LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C  LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  parallel stats graphics grDevices utils datasets methods base other attached packages:  beadarray_2.24.0 ggplot2_2.2.1 Biobase_2.34.0 BiocGenerics_0.20.0 loaded via a namespace (and not attached):  Rcpp_0.12.10 AnnotationDbi_1.36.2 XVector_0.14.1 magrittr_1.5  GenomicRanges_1.26.4 zlibbioc_1.20.0 IRanges_2.8.2 munsell_0.4.3  colorspace_1.3-2 stringr_1.2.0 GenomeInfoDb_1.10.3 plyr_1.8.4  tools_3.4.0 grid_3.4.0 base64_2.0 gtable_0.2.0  DBI_0.6-1 lazyeval_0.2.0 openssl_0.9.6 digest_0.6.12  tibble_1.3.0 reshape2_1.4.2 S4Vectors_0.12.2 bitops_1.0-6  RCurl_1.95-4.8 memoise_1.1.0 RSQLite_1.1-2 limma_3.30.13  stringi_1.1.5 BeadDataPackR_1.26.0 compiler_3.4.0 scales_0.4.1  stats4_3.4.0 illuminaio_0.16.0