search

gabrielodom / pathwayPCA

integrative pathway analysis with modern PCA methodology and gene selection
https://gabrielodom.github.io/pathwayPCA/
11 stars 2 forks source link

function createOmics #84

Closed lizhongliu1996 closed 4 years ago

lizhongliu1996 commented 5 years ago

createOmics fail to show message that There is 0 sample shared by the assay and phenotype data.

the assay data has sample column head(ovmRNA_df$Sample) [1] "TCGA-24-1850-01A-01R-1567-13" "TCGA-61-2104-01A-01R-1568-13" "TCGA-24-1470-01A-01R-1566-13" "TCGA-61-1741-01A-02R-1567-13" [5] "TCGA-24-2023-01A-01R-1567-13" "TCGA-13-0762-01A-01R-1564-13"

the response has sample column Sample <chr> 1 TCGA-3P-A9WA 2 TCGA-59-A5PD 3 TCGA-5X-AA5U 4 TCGA-04-1331 5 TCGA-04-1332 6 TCGA-04-1335 7 TCGA-04-1336 8 TCGA-04-1337 9 TCGA-04-1338 10 TCGA-04-1341

gabrielodom commented 4 years ago

The TCGA barcodes are not in the same form between assay and response. Your assay data is using a 22-digit barcode, while the response sample ID is using a 10-digit barcode.