Comments (2)
jhcreed
commented on July 30, 2024
For the Taylor et al. data (GSE21032) - using GEOquery contains mismatched information in the phenotype data. I have posted looking for help
https://community.rstudio.com/t/geoquery-getgeo-gse21032-pheno-data-mix-up/67546
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Syksy
commented on July 30, 2024
Taylor et al. is now curated from the two differing GEO instances (one for GEX, one for CNA), complemented by the mutation calls pulled for cBioPortal along with additional clinical information. sampleMap-function for the mae_taylor will contain mappings of IDs between differing platforms.
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Related Issues (20)
- Creation of sufficiently elaborate metadata for each MAE HOT 1
- Splitting apart OSF portion of TCGA HOT 2
- Purity Estimates HOT 2
- Abida et al focus on polyA / TCGA focus on TPM normalized GEX (OSF) HOT 1
- Risk score benchmarking HOT 1
- Gene ID aliases alter between datasets, especially older annotation ones HOT 2
- Row names HOT 1
- Benchmarking description HOT 1
- Double-checking ranks of newly normalized data HOT 1
- Include normal samples in Taylor et al. HOT 1
- Use the generic identifiers PCA#### / PAN#### in Taylor et al. HOT 1
- Sample IDs in Clinical data - Taylor et.al. HOT 2
- Fusion status HOT 1
- CNA and fusion sample size different in TCGA HOT 2
- Wang et al identifiers mismatch in derived variables HOT 1
- Weiner et al. & newly generated GEX for CIBERSORTx
- Cibersort results for Weiner et al. missing HOT 1
- colData does not work for MAE Barwick HOT 1
- Xenabrowser mapping not up to date HOT 1
- cBioPortal hg19 to hg38 liftOver HOT 1
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