Entering edit mode
Hi,
The following code used to work until yesterday evening (March 20th 2024).
The code downloads the PAAD TCGA data and extracts the z-score expression table.
Now, the loaded z-score expression table is filled with NA. There are also warnings during the download.
Has something changed in the way I should load this table?
Many thanks, Astrid
suppressPackageStartupMessages({
cbio <- cBioPortal()
paad <- cBioDataPack("paad_tcga", ask = FALSE)
})
Downloading study file: paad_tcga.tar.gz
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Working on: C:\Users\Astrid\AppData\Local\Temp\Rtmp2Xbnbe/d4056c13a62_paad_tcga/paad_tcga/data_cna.txt
Working on: C:\Users\Astrid\AppData\Local\Temp\Rtmp2Xbnbe/d4056c13a62_paad_tcga/paad_tcga/data_cna_hg19.seg
Working on: C:\Users\Astrid\AppData\Local\Temp\Rtmp2Xbnbe/d4056c13a62_paad_tcga/paad_tcga/data_linear_cna.txt
Working on: C:\Users\Astrid\AppData\Local\Temp\Rtmp2Xbnbe/d4056c13a62_paad_tcga/paad_tcga/data_methylation_hm450.txt
Working on: C:\Users\Astrid\AppData\Local\Temp\Rtmp2Xbnbe/d4056c13a62_paad_tcga/paad_tcga/data_mrna_seq_v2_rsem.txt
Working on: C:\Users\Astrid\AppData\Local\Temp\Rtmp2Xbnbe/d4056c13a62_paad_tcga/paad_tcga/data_mrna_seq_v2_rsem_zscores_ref_all_samples.txt
Working on: C:\Users\Astrid\AppData\Local\Temp\Rtmp2Xbnbe/d4056c13a62_paad_tcga/paad_tcga/data_mrna_seq_v2_rsem_zscores_ref_diploid_samples.txt
Working on: C:\Users\Astrid\AppData\Local\Temp\Rtmp2Xbnbe/d4056c13a62_paad_tcga/paad_tcga/data_mutations.txt
Working on: C:\Users\Astrid\AppData\Local\Temp\Rtmp2Xbnbe/d4056c13a62_paad_tcga/paad_tcga/data_rppa.txt
Working on: C:\Users\Astrid\AppData\Local\Temp\Rtmp2Xbnbe/d4056c13a62_paad_tcga/paad_tcga/data_rppa_zscores.txt
Warning messages:
1: In .find_with_xfix(df_colnames, get(paste0(fix, 1)), get(paste0(fix, :
Multiple prefixes found, using keyword 'region' or taking first one
2: In .find_with_xfix(df_colnames, get(paste0(fix, 1)), get(paste0(fix, :
Multiple prefixes found, using keyword 'region' or taking first one
expRNAseqAllZscores <- experiments(paad)[8][[1]]
expRNA <- assays(expRNAseqAllZscores)[[1]]
head(expRNA)
TCGA-2J-AAB1-01 TCGA-2J-AABE-01 TCGA-2J-AABU-01 TCGA-2L-AAQL-01 TCGA-3A-A9IC-01 TCGA-3A-A9J0-01
EXPH5 NA NA NA NA NA NA
MBD6 NA NA NA NA NA NA
PLEK NA NA NA NA NA NA
NT5C2 NA NA NA NA NA NA
WDR37 NA NA NA NA NA NA
NEBL NA NA NA NA NA NA
> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=English_Canada.utf8 LC_CTYPE=English_Canada.utf8 LC_MONETARY=English_Canada.utf8
[4] LC_NUMERIC=C LC_TIME=English_Canada.utf8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] survminer_0.4.9 ggpubr_0.6.0 ggplot2_3.4.4
[4] survival_3.5-7 org.Hs.eg.db_3.18.0 AnnotationDbi_1.63.2
[7] cBioPortalData_2.14.2 MultiAssayExperiment_1.28.0 SummarizedExperiment_1.31.1
[10] Biobase_2.61.0 GenomicRanges_1.53.2 GenomeInfoDb_1.37.6
[13] IRanges_2.35.3 S4Vectors_0.39.3 BiocGenerics_0.47.0
[16] MatrixGenerics_1.13.1 matrixStats_1.0.0 AnVIL_1.14.2
[19] dplyr_1.1.3
loaded via a namespace (and not attached):
[1] rstudioapi_0.15.0 jsonlite_1.8.7 magrittr_2.0.3
[4] GenomicFeatures_1.53.2 rmarkdown_2.25 BiocIO_1.11.0
[7] zlibbioc_1.47.0 vctrs_0.6.4 memoise_2.0.1
[10] Rsamtools_2.17.0 RCurl_1.98-1.12 rstatix_0.7.2
[13] BiocBaseUtils_1.3.2 htmltools_0.5.6 S4Arrays_1.1.6
[16] progress_1.2.2 lambda.r_1.2.4 curl_5.2.0
[19] broom_1.0.5 SparseArray_1.1.12 htmlwidgets_1.6.2
[22] zoo_1.8-12 futile.options_1.0.1 cachem_1.0.8
[25] GenomicAlignments_1.37.0 mime_0.12 lifecycle_1.0.3
[28] pkgconfig_2.0.3 Matrix_1.6-1.1 R6_2.5.1
[31] fastmap_1.1.1 GenomeInfoDbData_1.2.10 shiny_1.7.5.1
[34] digest_0.6.33 colorspace_2.1-0 RaggedExperiment_1.26.0
[37] RSQLite_2.3.1 filelock_1.0.2 RTCGAToolbox_2.32.1
[40] km.ci_0.5-6 fansi_1.0.4 RJSONIO_1.3-1.8
[43] httr_1.4.7 abind_1.4-5 compiler_4.3.1
[46] withr_2.5.1 bit64_4.0.5 backports_1.4.1
[49] BiocParallel_1.35.4 carData_3.0-5 DBI_1.1.3
[52] ggsignif_0.6.4 biomaRt_2.57.1 rappdirs_0.3.3
[55] DelayedArray_0.27.10 rjson_0.2.21 tools_4.3.1
[58] httpuv_1.6.11 glue_1.6.2 restfulr_0.0.15
[61] promises_1.2.1 grid_4.3.1 generics_0.1.3
[64] gtable_0.3.4 KMsurv_0.1-5 tzdb_0.4.0
[67] tidyr_1.3.0 data.table_1.14.8 hms_1.1.3
[70] car_3.1-2 xml2_1.3.5 utf8_1.2.3
[73] XVector_0.41.1 pillar_1.9.0 stringr_1.5.0
[76] later_1.3.1 splines_4.3.1 BiocFileCache_2.9.1
[79] lattice_0.21-8 rtracklayer_1.61.1 bit_4.0.5
[82] tidyselect_1.2.0 Biostrings_2.69.2 miniUI_0.1.1.1
[85] knitr_1.44 gridExtra_2.3 futile.logger_1.4.3
[88] xfun_0.40 DT_0.30 stringi_1.7.12
[91] yaml_2.3.7 evaluate_0.22 codetools_0.2-19
[94] tibble_3.2.1 cli_3.6.1 xtable_1.8-4
[97] munsell_0.5.0 survMisc_0.5.6 Rcpp_1.0.11
[100] GenomicDataCommons_1.26.0 dbplyr_2.3.4 png_0.1-8
[103] XML_3.99-0.14 rapiclient_0.1.3 parallel_4.3.1
[106] TCGAutils_1.22.2 ellipsis_0.3.2 readr_2.1.4
[109] blob_1.2.4 prettyunits_1.2.0 bitops_1.0-7
[112] scales_1.2.1 purrr_1.0.2 crayon_1.5.2
[115] rlang_1.1.1 KEGGREST_1.41.4 rvest_1.0.3
[118] formatR_1.14
Hi Astrid,
I took a look at the
data_mutations.txtand it looks like theEntrez_Gene_Idcolumn is allNA.FWIW, you can use
downloadStudyand thenuntarto investigate the data in the files.Note that
paad[["mutations"]]is aRaggedExperimentand it only represents the first column in themcols.To represent a different column, you can use the
iargument inassay:For more transformations, see the
RaggedExperimentvignette and the?RaggedExperiment::`assay-functions` documentation page.Best regards,
Marcel
Hi Marcel,
Thanks for the quick answer.
To look at the z-score expression, I need to extract
experiments(paad)[6]instead ofexperiments(paad)[8].Has the order changed?
Best, Astrid
Hi Astrid,
Please always use named rather than numeric indices. It avoids issues as above. For me, experiment #8 is
mutations.I suppose you meant to refer to :
-Marcel