comparison rgedgeR/rgedgeRpaired.xml @ 17:b1cf0745bde5 draft

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16:cddf60746340

    <conditional name="DESeq2">
    <param name="doDESeq2" type="select" 
       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>
     </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>
         </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">
      <option value="F" selected="true">Do not run VOOM</option>
      <option value="T">Run VOOM</option>
     </param>
    <param name="fdrthresh" type="float" value="0.05" size="5" label="P value threshold for FDR filtering for amily wise error rate control"
     help="Conventional default value of 0.05 recommended"/>

#if $edgeR.doedgeR == "T":
  out_edgeR = "$out_edgeR"
  edgeR_priordf = $edgeR.edgeR_priordf
#end if

Out_Dir = "$html_file.files_path"
Input =  "$input1"
TreatmentName = "$treatment_name"
TreatmentCols = "$Treat_cols"
ControlName = "$control_name"

useNDF = $useNDF
fQ = $fQ # non-differential centile cutoff
myTitle = "$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=')
cat(TCols)
cat('; CCols=')

17:b1cf0745bde5

    <conditional name="DESeq2">
    <param name="doDESeq2" type="select" 
       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</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 - 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="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>
    <param name="fdrthresh" type="float" value="0.05" size="5" label="P value threshold for FDR filtering for amily wise error rate control"
     help="Conventional default value of 0.05 recommended"/>

#if $edgeR.doedgeR == "T":
  out_edgeR = "$out_edgeR"
  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 = "$treatment_name"
TreatmentCols = "$Treat_cols"
ControlName = "$control_name"

useNDF = $useNDF
fQ = $fQ # non-differential centile cutoff
myTitle = "$title"
subjects = c($subjectids)
nsubj = length(subjects)
TCols = as.numeric(strsplit(TreatmentCols,",")[[1]])-1
CCols = as.numeric(strsplit(ControlCols,",")[[1]])-1 
cat('Got TCols=')
cat(TCols)
cat('; CCols=')