Hi all! I have used ChAMP a bunch over the last six or so years to analyze EPIC array data (thank you, Yuan Tian, for such a great package!). However, I just back my first EPIC v2 dataset. I read on the github (https://github.com/YuanTian1991/ChAMP-DemoRun/tree/main/EPICv2/illumina_demo_data_iScan) that I need to install the latest version of ChAMP and ChAMPdata and extract the correct manifest from ChAMPdata using data(AnnoEPICv2).
However, even having done, this I get an error after the Extracting UnMeth Matrix step using champ.import() or champ.load() specifying arraytype="EPICv2":
My exact commands (both give same error):
datload <- champ.load(basedir,arraytype="EPICv2")
datimport <- champ.import(directory=basedir, arraytype="EPICv2")
error:
Error in champ.import(directory, arraytype = arraytype) :
Meth Matrix and UnMeth Matrix seems not paried correctly.
When I don't specify, arraytype="EPICv2" but just arraytype="EPIC" I get a little further, with ChAMP actually outputting the fraction of failed probes.
But, after the Filtering SNPs Start step, I still get the error
Error in champ.filter(beta = myImport$beta, M = NULL, pd = myImport$pd, :
object 'EPIC.manifest.hg19' not found
In addition: Warning messages:
1: In data(AnnoEPIC) : data set 'AnnoEPIC' not found
2: In data(EPIC.manifest.hg19) : data set 'EPIC.manifest.hg19' not found
My specific command:
datload <- champ.load(basedir,arraytype="EPIC")
Any thoughts why I am stuck?? THANK YOU!!
sessionInfo( )
R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
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
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] IlluminaHumanMethylationEPICv2anno.20a1.hg38_1.0.0
[2] IlluminaHumanMethylationEPICv2manifest_1.0.0
[3] ChAMP_2.29.1
[4] RPMM_1.25
[5] cluster_2.1.6
[6] DT_0.33
[7] IlluminaHumanMethylationEPICmanifest_0.3.0
[8] Illumina450ProbeVariants.db_1.40.0
[9] DMRcate_3.0.10
[10] ChAMPdata_2.31.1
[11] minfi_1.50.0
[12] bumphunter_1.46.0
[13] locfit_1.5-9.9
[14] iterators_1.0.14
[15] foreach_1.5.2
[16] Biostrings_2.72.0
[17] XVector_0.44.0
[18] SummarizedExperiment_1.34.0
[19] Biobase_2.64.0
[20] MatrixGenerics_1.16.0
[21] matrixStats_1.3.0
[22] GenomicRanges_1.56.0
[23] GenomeInfoDb_1.40.0
[24] IRanges_2.38.0
[25] S4Vectors_0.42.0
[26] BiocGenerics_0.50.0
[27] BiocManager_1.30.22
[28] lubridate_1.9.3
[29] forcats_1.0.0
[30] stringr_1.5.1
[31] dplyr_1.1.4
[32] purrr_1.0.2
[33] readr_2.1.5
[34] tidyr_1.3.1
[35] tibble_3.2.1
[36] ggplot2_3.5.0
[37] tidyverse_2.0.0
