Running ENmix with mouse methylation manifest: readidat error - Error in readmanifest(manifestfile) : length(control.line) == 1 && is.integer(control.line) && !is.na(control.line) is not TRUE
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minardsmitha ▴ 10
@minardsmitha-24162
Last seen 17 days ago
United States

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
ENmix Bioconductor • 525 views
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Entering edit mode
minardsmitha ▴ 10
@minardsmitha-24162
Last seen 17 days ago
United States

Well it turns out there is a typo in the manifest file name. This particular issue is resolved by correcting the typo.
A new error now appears that I will try to figure out on my own. If I can't resolve the new error I will start a new question.

rgSet <- readidat(path = getwd(),manifestfile=mf,recursive = TRUE)
[readidat] Found 210 files with suffix _Grn.idat
[readidat] Found 210 files with suffix _Red.idat
Error in `$<-.data.frame`(`*tmp*`, "Infinium_Design_Type", value = "A") : 
  replacement has 1 row, data has 0
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Hi, I am having the same issues. What was the typo that you found? And were you able to solve the next problem?

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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?

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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"

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0
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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.

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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.

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