What it does

Generate input files required for GSEA analysis.

Parameters

- Title to personalize output file names (please avoid special characters).

- GSEA configuration : "GSEA analysis" requires expression dataset and phenotype label for each sample whereas "Pre-ranked GSEA Analysis" needs ranked list of samples extracted from differential analysis results.

• GSEA Analysis

  - Expression tabular file with samples as columns and genes as rows (header row contains sample names and first column gene identifiers).

  Conditions  157_(HuGene-2_0-st).CEL 156_(HuGene-2_0-st).CEL  155_(HuGene-2_0-st).CEL    154_(HuGene-2_0-st).CEL
  DDX11L2     4.500872                4.429759                 4.780281                   4.996189
  MIR1302-2   3.415065                3.520472                 3.471503                   3.567988
  OR4F5       3.737956                3.011586                 3.424494                   3.497545
  VWA1        5.189621                5.129595                 4.806793                   5.227014
  

  - Factor information tabular file with factors as columns and samples as rows (header row contains factor names and first column sample names).

  Conditions                Sex   Treatment Reaction
  138_(HuGene-2_0-st).CEL   1     TreatA    Pos
  148_(HuGene-2_0-st).CEL   0     NoTreat   Pos
  139_(HuGene-2_0-st).CEL   0     TreatB    Neg
  149_(HuGene-2_0-st).CEL   0     NoTreat   Neg
  

  - Reference factor to use as phenotype in GSEA amongst available factors in factor information file.

• Pre-ranked GSEA Analysis

  - Differential analysis tabular file with contrasts statistics (p-val, FDR p-val, FC, log2(FC) and moderated t-statistic) as columns and genes as rows (first and second rows contain contrasts definition and first and second columns contain gene identifiers and functional informations). Please respect the GIANT-Differential Expression Analysis with LIMMA tool output format.

  LIMMA    comparison  WT*Treat  WT*Treat  WT*Treat  WT*Treat  WT*Treat
  Gene     Info        p-val     FDR.p-val FC        log2(FC)  t-stat
  ARSD     na          0.0057    0.41      0.8389   -0.2534   -5.175
  TTTY10   na          1.6e-07   0.0074    0.6403   -0.6432   -6.122
  MIR548AL na          0.072     0.2914    1.711     0.775     10.43
  

  - Reference contrast from available contrasts in differential analysis file to use for gene ranking.

  - Reference statistic from reference contrast used to rank genes. Relative or absolute value of log2(FC) or moderated t-statistic is used to sort genes in a decreasing way.

  - FDR p-val threshold to discard genes with higher FDR p-val than specific threshold [0.05 recommended]. Genes with high FDR p-val are not significant for differential expression in reference contrast.

Outputs

Depends on GSEA configuration:

• GSEA Analysis

  - phenotype file (.cls) to use as "phenotype labels" file for GSEA.

  - expression file (.gct) to use as "expression dataset" file for GSEA.

• Pre-ranked GSEA Analysis

  - pre-ranked file (.rnk) to use as "ranked list" file for GSEA pre-ranked.

For all configurations:

- LOG file containing information about execution. Useful especially if tool execution fails. Please attach this log file in any bug report.