... | ... | @@ -292,12 +292,12 @@ In the main folder are located the files common to all comparisons. This is a de |
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For each comparisons specified in *[the comparisons file](usage/inputs#compFile)*, a folder named **condition1__vs__condition2** is created. All files within this folder refers to this comparison only:
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- "DEseqRes.tsv" : results of deseq2. Each line is the result of the statistical test determining if the gene is differentially expressed or not.
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- "DEseqResFiltered.tsv" : same as above but only on genes considered differentially expressed according to the threshold of adjusted p-value (0.05) and logFC (0.58).
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- "DEseqResFiltered.tsv" : same as above but only on genes considered differentially expressed according to the threshold of adjusted p-value (0.05) and logFC (0.58 by default).
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- "MA-plot.png", "Volcano-plot.png" : representations of the differentially expressed genes.
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- "clustDEgene.png" : heatmap of the differentially expressed genes for the samples included in the comparison only.
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- "clustDEgene.pdf" : same as above enriched with a heatmap of the differentially expressed genes for all samples of the project.
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![DE Analysis](../images/deAnalysis.png)
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![DE Analysis](images/deAnalysis.png)
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The other files of this folder are results of tertiary analysis tools. They give an insight on the meaning of the list of differentially expressed genes.
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... | ... | @@ -306,7 +306,7 @@ For each comparisons specified in *[the comparisons file](usage/inputs#compFile) |
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- "gseGo.txt", "gseKegg.txt" : Gene Set Enrichment Analysis (GSEA) results for Gene Ontology and Kegg Pathways. You can find all about GSEA analysis on the [Broad Institut GSEA page](https://www.gsea-msigdb.org/gsea/index.jsp).
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- "stringFunctionalEnrichment.tsv" : ORA analysis from the [STRING-DB](https://string-db.org/) database.
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![Tertiary Analysis](../images/terAnalysis.png)
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![Tertiary Analysis](images/terAnalysis.png)
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## The final report
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