changeset 17:b1cf0745bde5 draft

Uploaded

--- a/rgedgeR/rgedgeRpaired.xml	Sat Jul 27 04:19:51 2013 -0400
+++ b/rgedgeR/rgedgeRpaired.xml	Sat Jul 27 20:35:56 2013 -0400
@@ -61,20 +61,20 @@
        label="Run the same model with DESeq2 and compare findings"
        help="DESeq2 is an update to the DESeq package. It uses different assumptions and methods to edgeR">
       <option value="F" selected="true">Do not run DESeq2</option>
-      <option value="T">Run DESeq2 (only works if NO second GLM factor supplied at present)</option>
+      <option value="T">Run DESeq2</option>
      </param>
      <when value="T">
          <param name="DESeq_fitType" type="select">
             <option value="parametric" selected="true">Parametric (default) fit for dispersions</option>
-            <option value="local">Local fit - use this if parametric fails</option>
-            <option value="mean">Mean dispersion fit- use this if you really understand what you're doing - read the fine manual</option>
+            <option value="local">Local fit - this will automagically be used if parametric fit fails</option>
+            <option value="mean">Mean dispersion fit- use this if you really understand what you're doing - read the fine manual linked below in the documentation</option>
          </param> 
      </when>
      <when value="F"> </when>
     </conditional>
     <param name="doVoom" type="select" 
        label="Run the same model with Voom/limma and compare findings"
-       help="The VOOM transformation allows analysis of count data using limma">
+       help="Voom uses counts per million and a precise transformation of variance so count data can be analysed using limma">
       <option value="F" selected="true">Do not run VOOM</option>
       <option value="T">Run VOOM</option>
      </param>
@@ -691,6 +691,12 @@
   edgeR_priordf = $edgeR.edgeR_priordf
 #end if
 
+if (sum(c(doedgeR,doVoom,doDESeq2)) == 0)
+{
+write("No methods chosen - nothing to do! Please try again after choosing one or more methods", stderr())
+quit(save="no")
+}
+
 Out_Dir = "$html_file.files_path"
 Input =  "$input1"
 TreatmentName = "$treatment_name"
@@ -706,12 +712,6 @@
 myTitle = "$title"
 subjects = c($subjectids)
 nsubj = length(subjects)
-if (nsubj > 0) {
-if (doDESeq2) {
- print('WARNING - cannot yet use DESeq2 for 2 way anova - see the docs')
- doDESeq2 = F
- }
-}
 TCols = as.numeric(strsplit(TreatmentCols,",")[[1]])-1
 CCols = as.numeric(strsplit(ControlCols,",")[[1]])-1 
 cat('Got TCols=')