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Merge pull request #105 from RabeaMue/patch-1
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Update 13-data-qc.md Fix links
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cpauvert authored Feb 15, 2024
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- **source**: Dim. reduction embedding, negative control study
- **possible reason(s)**: use raw data for tSNE/UMAP
- **solution/measure**: use a significant portion of PC from the PCA as input for tSNE/UMAP
3. "The first two principle components were used to perform a tSNE" (https://www.science.org/doi/full/10.1126/science.aag3009)
3. "The first two principle components were used to perform a tSNE" [https://www.science.org/doi/full/10.1126/science.aag3009](https://www.science.org/doi/full/10.1126/science.aag3009)
- **source**: Dim. reduction embedding, negative control study
- **possible reason(s)**: use only 2 PC from the PCA for the tSNE/UMAP projection
- **solution/measure**: use a significant portion of PC from the PCA as input for tSNE/UMAP
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- **solution/measure**: use a population size cutoff or state the number
2. some genes look like dates (1-Mar,...)
- **source**: seurat/deseq, negative control study
- **possible reason(s)**: some genes can be interpreted as dates when using excel for data handling (https://www.science.org/doi/10.1126/science.aah4573)
- **possible reason(s)**: some genes can be interpreted as dates when using excel for data handling [https://www.science.org/doi/10.1126/science.aah4573](https://www.science.org/doi/10.1126/science.aah4573)
- **solution/measure**: never ever use excel or at least make sure that cell type is not "AUTO"

# Further resources
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