Hi,
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.
Googling I found this document: https://support.illumina.com/bulletins/2016/10/important-information-about-using-digit-beadchip-barcodes-in-genomestudio-sample-sheets.html
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
Simon
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: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] beadarray_2.24.0 ggplot2_2.2.1 Biobase_2.34.0 BiocGenerics_0.20.0 loaded via a namespace (and not attached): [1] Rcpp_0.12.10 AnnotationDbi_1.36.2 XVector_0.14.1 magrittr_1.5 [5] GenomicRanges_1.26.4 zlibbioc_1.20.0 IRanges_2.8.2 munsell_0.4.3 [9] colorspace_1.3-2 stringr_1.2.0 GenomeInfoDb_1.10.3 plyr_1.8.4 [13] tools_3.4.0 grid_3.4.0 base64_2.0 gtable_0.2.0 [17] DBI_0.6-1 lazyeval_0.2.0 openssl_0.9.6 digest_0.6.12 [21] tibble_1.3.0 reshape2_1.4.2 S4Vectors_0.12.2 bitops_1.0-6 [25] RCurl_1.95-4.8 memoise_1.1.0 RSQLite_1.1-2 limma_3.30.13 [29] stringi_1.1.5 BeadDataPackR_1.26.0 compiler_3.4.0 scales_0.4.1 [33] stats4_3.4.0 illuminaio_0.16.0
Hi Mark,
thanks for your reply!
I managed to get it working - at least as long as I don't specify
useImages
inreadIllumina().
I had to change summarize() as well, the attached diffs work for my dataset (see below), though I can't say anything about backward compatibility with older, shorter chip IDs.
One thing that is still not working is using the TIFFs directly.
Diff for summarize:
Diff for readIllumina:
Additionally, this is the structure of the zipped folders I receive from our core facility:
(This is just for one chip due to space constraints here in the commenting system, chips range from A to L, of course)
I think it's interesting that there are XMLs for a red channel which is AFAIR not present on Illumina's HT12 chips. I had to remove them from the directory, otherwise beadarray gets confused and tries to read 2-channel data.