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Update docs/output.md
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Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com>
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rezaeinfo and pinin4fjords committed Mar 20, 2024
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Expand Up @@ -63,7 +63,7 @@ Most plots are included in the HTML report (see above), but are also included in
- `[array platform].annotation.tsv`: Annotations derived from an array platform
- `[GTF name].anno.tsv`: Species wise annotations derived from a GTF in RNA-seq analysis
- `processed_abundance/`: Directory containing processed abundance values from initial processing from e.g. DESeq2 or Affy:
- `[contrast_name].normalised_counts.tsv`: Normalized counts table (DESeq2). Rows are Ensembl IDs and columns are samples.
- `[contrast_name].normalised_counts.tsv`: Normalised counts table (DESeq2). Rows are feature (e.g. gene) IDs and columns are observations (e.g. samples).
- `[contrast_name].vst.tsv`: Normalised counts table with a variance-stabilising transform (DESeq2)
- `raw.matrix.tsv`: RMA background corrected matrix (Affy)
- `normalised.matrix.tsv`: RMA background corrected and normalised intensities matrix (Affy)
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