diff --git a/docs/output.md b/docs/output.md index 1be87c9b..3a58d4d8 100644 --- a/docs/output.md +++ b/docs/output.md @@ -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)