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cmap / cmapR

Tools for manipulating annotated data matrices
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parse_gctx throwing error which I am not able to understand #69

Open jjyotikataria opened 2 years ago

jjyotikataria commented 2 years ago

parse_gctx is not able to read the gct file for me with this command. cmap version is cmapR_1.9.0 .

parse_gctx("BLM_Aged_n83x18577.gct") parsing as GCT v1.2 BLM_Aged_n83x18577.gct NA rows, NA cols, 0 row descriptors, 0 col descriptors Error in matrix(m, nrow = nrmat, ncol = ncmat + nrhd + col_offset, byrow = TRUE) : invalid 'nrow' value (too large or NA)

sessioninfo()

R version 4.1.2 (2021-11-01) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.6

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages: [1] rhdf5_2.38.1 CePa_0.8.0 shiny_1.7.1 gridExtra_2.3 biomaRt_2.50.3
[6] scales_1.2.0 ggpubr_0.4.0.999 ggplot2_3.3.5 tidyr_1.2.0 dplyr_1.0.9
[11] GEOquery_2.62.2 cmapR_1.9.0 GSEABase_1.56.0 graph_1.72.0 annotate_1.72.0
[16] XML_3.99-0.8 AnnotationDbi_1.56.2 IRanges_2.28.0 S4Vectors_0.32.4 Biobase_2.54.0
[21] BiocGenerics_0.40.0 limma_3.50.0

loaded via a namespace (and not attached): [1] colorspace_2.0-2 ggsignif_0.6.3 ellipsis_0.3.2 cytolib_2.6.2
[5] XVector_0.34.0 GenomicRanges_1.46.1 rstudioapi_0.13 ggrepel_0.9.1
[9] bit64_4.0.5 fansi_1.0.3 xml2_1.3.3 cachem_1.0.6
[13] jsonlite_1.8.0 broom_0.7.12 dbplyr_2.2.0 png_0.1-7
[17] BiocManager_1.30.18 readr_2.1.2 compiler_4.1.2 httr_1.4.3
[21] backports_1.4.1 assertthat_0.2.1 Matrix_1.3-4 fastmap_1.1.0
[25] cli_3.3.0 later_1.3.0 htmltools_0.5.2 prettyunits_1.1.1
[29] tools_4.1.2 igraph_1.2.11 gtable_0.3.0 glue_1.6.2
[33] GenomeInfoDbData_1.2.7 rappdirs_0.3.3 Rcpp_1.0.8.3 carData_3.0-5
[37] jquerylib_0.1.4 vctrs_0.4.1 Biostrings_2.62.0 rhdf5filters_1.6.0
[41] stringr_1.4.0 mime_0.12 lifecycle_1.0.1 rstatix_0.7.0
[45] zlibbioc_1.40.0 RProtoBufLib_2.6.0 hms_1.1.1 promises_1.2.0.1
[49] MatrixGenerics_1.6.0 parallel_4.1.2 SummarizedExperiment_1.24.0 curl_4.3.2
[53] memoise_2.0.1 sass_0.4.1 stringi_1.7.6 RSQLite_2.2.14
[57] flowCore_2.6.0 filelock_1.0.2 GenomeInfoDb_1.30.1 rlang_1.0.2
[61] pkgconfig_2.0.3 matrixStats_0.62.0 bitops_1.0-7 lattice_0.20-45
[65] purrr_0.3.4 Rhdf5lib_1.16.0 bit_4.0.4 tidyselect_1.1.2
[69] magrittr_2.0.3 R6_2.5.1 generics_0.1.2 DelayedArray_0.20.0
[73] DBI_1.1.2 pillar_1.7.0 withr_2.5.0 KEGGREST_1.34.0
[77] abind_1.4-5 RCurl_1.98-1.6 tibble_3.1.7 crayon_1.5.1
[81] car_3.0-12 utf8_1.2.2 BiocFileCache_2.2.1 tzdb_0.2.0
[85] progress_1.2.2 grid_4.1.2 data.table_1.14.2 blob_1.2.3
[89] Rgraphviz_2.38.0 digest_0.6.29 xtable_1.8-4 httpuv_1.6.5
[93] RcppParallel_5.1.5 munsell_0.5.0 bslib_0.3.1

@kant @jasiedu @tnat1031 Could you please help?

tnat1031 commented 2 years ago

Hi @jjyotikataria, are you able to share the GCT file you're trying to parse?

jjyotikataria commented 2 years ago

@tnat1031 Can't share the gct because of official reasons. Is there any other way round to fix this as I am not able to proceed for analyzing expression data because the file is not being read.

tnat1031 commented 2 years ago

@jjyotikataria Sure, I understand. Would you be able to send the first 10 lines of the file? Even as a screenshot?