@@ -1,6 +1,6 @@

 Package: ReportingTools

 Title: Tools for making reports in various formats

-Version: 2.17.3

+Version: 2.17.4

 Author: Jason A. Hackney, Melanie Huntley, Jessica L. Larson, Christina

         Chaivorapol, Gabriel Becker, and Josh Kaminker

 Maintainer: Jason A. Hackney <hackney.jason@gene.com>, Gabriel Becker

@@ -23,14 +23,14 @@ setMethod("publish",

 {

     dat <- topTags(object, n = n, adjust.method = adjust.method, 

         sort.by = sort.method)

-

-    if(!is.null(object$genes) & all(rownames(object$genes) == 

-            as.character(seq_along(rownames(object$genes))))){

-        selection <- as.numeric(rownames(dat$table))

-        selection <- rownames(object$table)[selection]

-    } else {

-        selection <- rownames(dat$table)

-    }

+    

+    # if(!is.null(object$genes) & all(rownames(object$genes) ==

+    #         as.character(seq_along(rownames(object$genes))))){

+    #     selection <- as.numeric(rownames(dat$table))

+    #     selection <- rownames(object$table)[selection]

+    # } else {

+    selection <- rownames(dat$table)

+    # }

     ##The following gives you all pvalues

     padj <- p.adjust(object$table$PValue, method = adjust.method)