Comments (4)
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Thanks - it's about differences in gene annotations and how they're structured in various databases, the ENSG-genes or ENST-transcripts don't have a 1:1 mapping to Hugo gene symbols, so in case of ambiguity or missing symbols, we'll most likely have to try either collapse multiple instances or omit genes without a gene symbol.
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Friedrich et al. has now been processed from raw data in v0.6.21 using limma pipeline for Agilent one-color arrays in generate.R, including the mapping to hugo symbols and collapsing probes while removing rows without hugo symbols.
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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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