I have a directory of idat files for 210 samples. I want to use ENmix to process this data. My data is from Mouse Methylation. I downloaded the mouse Illumina manifest file from https://support.illumina.com/downloads/infinium-mouse-methylation-manifest-file.html.
Then I ran the following code:
library(ENmix)
library(geneplotter)
library(limma)
mf="MouseMethylation_12v1-0_A2.csv"
rgSet <- readidat(path = getwd(),manifestfile=mf,recursive = TRUE)
Which produces this error message:
[readidat] Found 210 files with suffix _Grn.idat
[readidat] Found 210 files with suffix _Red.idat
Error in readmanifest(manifestfile) :
length(control.line) == 1 && is.integer(control.line) && !is.na(control.line) is not TRUE
In addition: Warning messages:
1: In system(sprintf("grep -n \\\\[Controls\\\\] %s", file), intern = TRUE) :
running command 'grep -n \\[Controls\\] MouseMethylation_12v1-0_A2.bpm' had status 2
2: In readmanifest(manifestfile) : NAs introduced by coercion
I have searched for a resolution to this issue and found a related post on here with no responses. I also looked at the code for readidat and see that it is finding the line in the manifest file that contains [Controls]. This line does exist in the manifest file.
Why am I getting this error and how can I fix it?
sessionInfo( )
R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] limma_3.54.2 geneplotter_1.76.0 annotate_1.76.0
[4] XML_3.99-0.16.1 AnnotationDbi_1.60.2 lattice_0.20-45
[7] ENmix_1.34.02 SummarizedExperiment_1.28.0 Biobase_2.58.0
[10] GenomicRanges_1.50.2 GenomeInfoDb_1.34.9 IRanges_2.32.0
[13] S4Vectors_0.36.2 BiocGenerics_0.44.0 MatrixGenerics_1.10.0
[16] matrixStats_1.3.0 doParallel_1.0.17 iterators_1.0.14
[19] foreach_1.5.2
loaded via a namespace (and not attached):
[1] AnnotationHub_3.6.0 BiocFileCache_2.13.0 plyr_1.8.9
[4] splines_4.2.2 BiocParallel_1.32.6 digest_0.6.35
[7] htmltools_0.5.8.1 RPMM_1.25 fansi_1.0.6
[10] magrittr_2.0.3 memoise_2.0.1 cluster_2.1.4
[13] tzdb_0.4.0 Biostrings_2.66.0 readr_2.1.5
[16] askpass_1.2.0 siggenes_1.72.0 prettyunits_1.2.0
[19] blob_1.2.4 rappdirs_0.3.3 dplyr_1.1.4
[22] crayon_1.5.2 RCurl_1.98-1.14 genefilter_1.80.3
[25] GEOquery_2.66.0 impute_1.72.3 survival_3.5-0
[28] glue_1.7.0 zlibbioc_1.44.0 XVector_0.38.0
[31] DelayedArray_0.24.0 Rhdf5lib_1.20.0 HDF5Array_1.26.0
[34] DBI_1.2.2 rngtools_1.5.2 Rcpp_1.0.12
[37] xtable_1.8-4 progress_1.2.3 bumphunter_1.40.0
[40] bit_4.0.5 mclust_6.1.1 preprocessCore_1.60.2
[43] httr_1.4.7 gplots_3.1.3.1 RColorBrewer_1.1-3
[46] pkgconfig_2.0.3 reshape_0.8.9 dbplyr_2.5.0
[49] locfit_1.5-9.9 utf8_1.2.4 dynamicTreeCut_1.63-1
[52] tidyselect_1.2.1 rlang_1.1.3 later_1.3.2
[55] BiocVersion_3.16.0 tools_4.2.2 cachem_1.0.8
[58] cli_3.6.2 generics_0.1.3 RSQLite_2.3.6
[61] ExperimentHub_2.6.0 stringr_1.5.1 fastmap_1.1.1
[64] yaml_2.3.8 bit64_4.0.5 beanplot_1.3.1
[67] caTools_1.18.2 scrime_1.3.5 purrr_1.0.2
[70] KEGGREST_1.38.0 nlme_3.1-162 doRNG_1.8.6
[73] sparseMatrixStats_1.10.0 mime_0.12 nor1mix_1.3-3
[76] xml2_1.3.6 biomaRt_2.54.1 compiler_4.2.2
[79] rstudioapi_0.16.0 filelock_1.0.3 curl_5.2.1
[82] png_0.1-8 interactiveDisplayBase_1.36.0 tibble_3.2.1
[85] stringi_1.8.4 GenomicFeatures_1.50.4 minfi_1.44.0
[88] Matrix_1.6-5 multtest_2.54.0 vctrs_0.6.5
[91] pillar_1.9.0 lifecycle_1.0.4 rhdf5filters_1.10.1
[94] BiocManager_1.30.23 data.table_1.15.4 bitops_1.0-7
[97] httpuv_1.6.15 rtracklayer_1.58.0 R6_2.5.1
[100] BiocIO_1.8.0 promises_1.3.0 KernSmooth_2.23-20
[103] codetools_0.2-19 pkgload_1.3.4 gtools_3.9.5
[106] MASS_7.3-58.2 rhdf5_2.42.1 openssl_2.1.2
[109] rjson_0.2.21 GenomicAlignments_1.34.1 Rsamtools_2.14.0
[112] GenomeInfoDbData_1.2.9 hms_1.1.3 quadprog_1.5-8
[115] grid_4.2.2 tidyr_1.3.1 base64_2.0.1
[118] DelayedMatrixStats_1.20.0 illuminaio_0.40.0 shiny_1.8.1.1
[121] restfulr_0.0.15
Hi, I am having the same issues. What was the typo that you found? And were you able to solve the next problem?
Could you try the following code and see whether you have any errors
mf="MouseMethylation-12v1-0_A2.csv"
manifest=readmanifest(mf)
What is the version of the ENmix that you used?
Thank you for the suggestion the ENmix version is using is ENmix_1.38.01.
I tried your suggested code, R identified the idat files but still returned the message below:
"[readidat] Found 20 files with suffix _Grn.idat [readidat] Found 20 files with suffix _Red.idat Error in system(command, as.integer(flag), f, stdout, stderr, timeout) : character string expected as first argument"
Could you try the latest version (1.40.1) to see how it works, I am not able to replicate the error message on my computer here.
I tried the latest version and encountered the same issues. The manifest file I downloaded is the .csv from the following link: https://emea.support.illumina.com/downloads/infinium-mouse-methylation-manifest-file.html Is this the correct version, or does there need to be some editing of the file to allow it to be read appropriately by R.