Some IDAT files are not present in the supplied base directory

[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

Originally posted by @jennyujin22 in #38 (comment)

[schmic05]

Dear Yujin, Can you share your sample annotation sheet and the output of ls in your idat directory? Also please show me the command that you use to start RnBeads. You can send this by email to michael.scherer at dkfz.de Best, Michael jennyujin22 ***@***.***> schrieb am Do., 9. Mai 2024, 09:22:

…

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 *Originally posted by @jennyujin22 <https://github.com/jennyujin22> in #38 (comment) <#38 (comment)>* — Reply to this email directly, view it on GitHub <#54>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADYQQ6CXHQNHA2PIQUUIVBTZBMP4XAVCNFSM6AAAAABHOKAWUKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGI4DOMBWHAZDGMA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[jennyujin22]

I sent it by email :)

Thanks a lot!