Entering edit mode
As the code block here , screenshot below.
It worked to get data from platform of Illumina Human Methylation 27 for TCGA-B6-A0IM. But, when I tried to change the platform argument to "Illumina Methylation Epic", it gave me an error as below. I assumed Epic may not be available. Firstly, I thought it may relate to the packages version. But, the error is still there after updating TCGAbiolinks to the lastest one.
So, my question is how should I know the platform availability for TCGA? Thanks!
query_met.hg38 <- GDCquery(
project = "TCGA-BRCA",
data.category = "DNA Methylation",
data.type = "Methylation Beta Value",
platform = "Illumina Methylation Epic",
barcode = c("TCGA-B6-A0IM")
)
# include your problematic code here with any corresponding output
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-BRCA
--------------------
oo Filtering results
--------------------
Error in GDCquery(project = "TCGA-BRCA", data.category = "DNA Methylation", :
Please set a valid platform argument from the list below:
=> Illumina Human Methylation 27
=> Illumina Human Methylation 450
other attached packages:
[1] GenomicRanges_1.56.2 GenomeInfoDb_1.40.1 IRanges_2.38.1 S4Vectors_0.42.1 sesameData_1.22.0 ExperimentHub_2.12.0
[7] AnnotationHub_3.12.0 BiocFileCache_2.12.0 dbplyr_2.5.0 BiocGenerics_0.50.0 TCGAbiolinks_2.32.0
loaded via a namespace (and not attached):
[1] DBI_1.2.3 httr2_1.0.5 biomaRt_2.60.1 rlang_1.1.4
[5] magrittr_2.0.3 matrixStats_1.4.1 compiler_4.4.1 RSQLite_2.3.7
[9] reshape2_1.4.4 png_0.1-8 vctrs_0.6.5 rvest_1.0.4
[13] stringr_1.5.1 pkgconfig_2.0.3 crayon_1.5.3 fastmap_1.2.0
[17] XVector_0.44.0 utf8_1.2.4 tzdb_0.4.0 preprocessCore_1.66.0
[21] UCSC.utils_1.0.0 purrr_1.0.2 bit_4.5.0 xfun_0.48
[25] zlibbioc_1.50.0 cachem_1.1.0 jsonlite_1.8.9 progress_1.2.3
[29] blob_1.2.4 DelayedArray_0.30.1 BiocParallel_1.38.0 parallel_4.4.1
[33] prettyunits_1.2.0 R6_2.5.1 stringi_1.8.4 RColorBrewer_1.1-3
[37] sesame_1.22.2 Rcpp_1.0.13 SummarizedExperiment_1.34.0 knitr_1.48
[41] wheatmap_0.2.0 downloader_0.4 R.utils_2.12.3 readr_2.1.5
[45] Matrix_1.7-0 tidyselect_1.2.1 abind_1.4-8 yaml_2.3.10
[49] codetools_0.2-20 curl_5.2.3 lattice_0.22-6 tibble_3.2.1
[53] plyr_1.8.9 Biobase_2.64.0 withr_3.0.1 KEGGREST_1.44.1
[57] xml2_1.3.6 Biostrings_2.72.1 pillar_1.9.0 BiocManager_1.30.25
[61] filelock_1.0.3 MatrixGenerics_1.16.0 generics_0.1.3 BiocVersion_3.19.1
[65] hms_1.1.3 ggplot2_3.5.1 munsell_0.5.1 scales_1.3.0
[69] glue_1.8.0 tools_4.4.1 data.table_1.16.2 XML_3.99-0.17
[73] grid_4.4.1 tidyr_1.3.1 AnnotationDbi_1.66.0 colorspace_2.1-1
[77] GenomeInfoDbData_1.2.12 cli_3.6.3 rappdirs_0.3.3 fansi_1.0.6
[81] S4Arrays_1.4.1 dplyr_1.1.4 gtable_0.3.5 R.methodsS3_1.8.2
[85] TCGAbiolinksGUI.data_1.24.0 digest_0.6.37 SparseArray_1.4.8 memoise_2.0.1
[89] R.oo_1.26.0 lifecycle_1.0.4 httr_1.4.7 mime_0.12
[93] bit64_4.5.2
Yes, it does. But, I mean how should I know in advance or where can I find the information before running code. Because I have several projects which need downloading. I'd like to avoid the error in my loop. Sorry for the confusion.