I am trying to figure out what information is provided by the gage() function. once the gage() function is produced, it provides three values (greater, less, stats). Under stats, it has stat.mean and exp1. I can't find any information on exp1 in the bioconductor manual I found here (https://bioconductor.org/packages/devel/bioc/manuals/gage/man/gage.pdf). Would anyone know what it means?

All the columns except for 'stat.mean' come from the input data. As an example, using the help page for gage:

 data(gse16873)
 cn=colnames(gse16873)
 hn=grep('HN',cn, ignore.case =TRUE)
 dcis=grep('DCIS',cn, ignore.case =TRUE)
 data(kegg.gs)
 data(go.gs)
#go.gs with the first 1000 entries as a fast example.
  gse16873.go.p <- gage(gse16873, gsets = go.gs, 
         ref = hn, samp = dcis)
> head(gse16873)
              HN_1   DCIS_1     HN_2   DCIS_2     HN_3   DCIS_3     HN_4
10000     6.765984 6.458339 6.921720 6.774493 7.010564 6.986779 6.958761
10001     6.339474 6.755342 7.177369 6.842597 7.392611 6.879474 6.296571
10002     6.591755 6.790304 6.735359 6.773255 6.700016 7.041881 6.586285
10003     6.822092 6.590539 6.508452 6.411859 6.575640 6.470913 6.896886
100048912 7.356051 7.311144 7.385513 7.333481 7.392233 7.428623 7.314579
10004     6.941935 6.854373 6.883973 6.833695 6.855043 6.856864 7.021072
            DCIS_4     HN_5   DCIS_5     HN_6   DCIS_6
10000     6.888199 6.949912 6.948589 7.220427 7.070159
10001     6.130034 7.831222 7.942344 7.665248 7.799255
10002     6.501011 6.884931 7.652490 7.342505 7.500791
10003     6.848872 6.615143 6.407087 6.618174 6.651619
100048912 7.362658 7.370044 7.397249 7.383196 7.437643
10004     7.051310 6.767242 6.775276 6.873855 6.805247

> colnames(gse16873.go.p$stats)
[1] "stat.mean" "DCIS_1"    "DCIS_2"    "DCIS_3"    "DCIS_4"    "DCIS_5"   
[7] "DCIS_6"