ERROR: Some IDAT files are not present in the supplied base directory

[TatiMoe]

Idat files and Sentrix_ID/Sentrix_Position in sample_annotation sheet match perfectly. Don´t understand why arror keeps coming... has anyone an idea? :(

[schmic05]

Hi Tati,

The error might arise from the conversion of the SentrixID in Excel from the number to the scientific notations (something like 5e+8). Otherwise, there might be some further mismatch. I would maybe recommend to specify the barcode column (i.e., SentrixID_SentrixPosition) directly.

Hope that helps,

Michael

[jennyujin22]

Dear Michael,

Even I already specify the barcode (SentrixID_SentrixPosition) and check if IDAT prefix is corresponding to barcode, there is an error "Some IDAT files are not present in the supplied base directory". (also I checked scientific notations).

here is my sessionInfo()

R version 4.4.0 (2024-04-24 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows 11 x64 (build 22631)

Matrix products: default

locale: [1] LC_COLLATE=Korean_Korea.utf8 LC_CTYPE=Korean_Korea.utf8 LC_MONETARY=Korean_Korea.utf8 LC_NUMERIC=C
[5] LC_TIME=Korean_Korea.utf8

time zone: Asia/Seoul tzcode source: internal

attached base packages: [1] parallel grid stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] RnBeads.hg19_1.36.0 RnBeads_2.22.0 plyr_1.8.9
[4] methylumi_2.50.0 minfi_1.50.0 bumphunter_1.46.0
[7] locfit_1.5-9.9 iterators_1.0.14 foreach_1.5.2
[10] Biostrings_2.72.0 XVector_0.44.0 SummarizedExperiment_1.34.0
[13] MatrixGenerics_1.16.0 FDb.InfiniumMethylation.hg19_2.2.0 org.Hs.eg.db_3.19.1
[16] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.56.0 AnnotationDbi_1.66.0
[19] reshape2_1.4.4 scales_1.3.0 Biobase_2.64.0
[22] illuminaio_0.46.0 matrixStats_1.3.0 limma_3.60.0
[25] gridExtra_2.3 gplots_3.1.3.1 ggplot2_3.5.1
[28] fields_15.2 viridisLite_0.4.2 spam_2.10-0
[31] ff_4.0.12 bit_4.0.5 cluster_2.1.6
[34] MASS_7.3-60.2 GenomicRanges_1.56.0 GenomeInfoDb_1.40.0
[37] IRanges_2.38.0 S4Vectors_0.41.6 sesame_1.22.0
[40] sesameData_1.22.0 ExperimentHub_2.12.0 AnnotationHub_3.12.0
[43] BiocFileCache_2.11.2 dbplyr_2.5.0 BiocGenerics_0.49.1

loaded via a namespace (and not attached): [1] RColorBrewer_1.1-3 rstudioapi_0.16.0 jsonlite_1.8.8 magrittr_2.0.3 BiocIO_1.14.0
[6] zlibbioc_1.50.0 vctrs_0.6.5 multtest_2.60.0 memoise_2.0.1 Rsamtools_2.20.0
[11] DelayedMatrixStats_1.26.0 RCurl_1.98-1.14 askpass_1.2.0 S4Arrays_1.4.0 curl_5.2.1
[16] Rhdf5lib_1.26.0 rhdf5_2.48.0 SparseArray_1.4.0 nor1mix_1.3-3 KernSmooth_2.23-22
[21] cachem_1.0.8 GenomicAlignments_1.40.0 lifecycle_1.0.4 pkgconfig_2.0.3 Matrix_1.7-0
[26] R6_2.5.1 fastmap_1.1.1 GenomeInfoDbData_1.2.12 digest_0.6.35 siggenes_1.78.0
[31] reshape_0.8.9 colorspace_2.1-0 RSQLite_2.3.6 base64_2.0.1 filelock_1.0.3
[36] fansi_1.0.6 beanplot_1.3.1 httr_1.4.7 abind_1.4-5 compiler_4.4.0
[41] rngtools_1.5.2 bit64_4.0.5 withr_3.0.0 BiocParallel_1.38.0 DBI_1.2.2
[46] HDF5Array_1.32.0 maps_3.4.2 openssl_2.1.2 rappdirs_0.3.3 DelayedArray_0.30.0
[51] rjson_0.2.21 gtools_3.9.5 caTools_1.18.2 tools_4.4.0 quadprog_1.5-8
[56] glue_1.7.0 restfulr_0.0.15 nlme_3.1-164 rhdf5filters_1.16.0 generics_0.1.3
[61] gtable_0.3.5 tzdb_0.4.0 preprocessCore_1.66.0 tidyr_1.3.1 data.table_1.15.4
[66] hms_1.1.3 xml2_1.3.6 utf8_1.2.4 BiocVersion_3.19.1 pillar_1.9.0
[71] stringr_1.5.1 genefilter_1.86.0 splines_4.4.0 dplyr_1.1.4 lattice_0.22-6
[76] survival_3.5-8 rtracklayer_1.64.0 GEOquery_2.72.0 annotate_1.82.0 tidyselect_1.2.1
[81] wheatmap_0.2.0 scrime_1.3.5 statmod_1.5.0 stringi_1.8.3 UCSC.utils_1.0.0
[86] yaml_2.3.8 codetools_0.2-20 tibble_3.2.1 BiocManager_1.30.23 cli_3.6.2
[91] xtable_1.8-4 munsell_0.5.1 Rcpp_1.0.12 png_0.1-8 XML_3.99-0.16.1
[96] readr_2.1.5 blob_1.2.4 mclust_6.1.1 dotCall64_1.1-1 doRNG_1.8.6
[101] sparseMatrixStats_1.16.0 bitops_1.0-7 purrr_1.0.2 crayon_1.5.2 rlang_1.1.3
[106] KEGGREST_1.44.0

Thanks a lot.

Best,

Yujin