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Allowed qn.bmiq and added help
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jenzopr committed Aug 31, 2016
1 parent 22496b5 commit dee3c17
Showing 1 changed file with 3 additions and 3 deletions.
6 changes: 3 additions & 3 deletions src/admire
Original file line number Diff line number Diff line change
Expand Up @@ -88,7 +88,7 @@ Available options:
Use multiple -r parameters to calculate for multiple region files
-p Detection p-value to exclude probes prior to analysis (0.01)
-t Exclude probes where more than t% samples failed according to the detection p-value. (0.5)
-n Normalization method (fn|swan|noob|illumina|raw|quantile)
-n Normalization method (fn|swan|noob|illumina|raw|quantile|qn.bmiq)
-b In case of functional normalization, skip noob background correction step
-d In case of noob or functional normalization, skip dye correction step
-f In case of quantile normalization, skip fixing outliers prior to analysis
Expand All @@ -113,10 +113,10 @@ EOL
g) G+=("$OPTARG")
;;
n)
if [[ "$OPTARG" == "fn" || "$OPTARG" == "noob" || "$OPTARG" == "illumina" || "$OPTARG" == "raw" || "$OPTARG" == "swan" || "$OPTARG" == "quantile" ]]; then
if [[ "$OPTARG" == "fn" || "$OPTARG" == "noob" || "$OPTARG" == "illumina" || "$OPTARG" == "raw" || "$OPTARG" == "swan" || "$OPTARG" == "quantile" || "$OPTARG" == "qn.bmiq" ]]; then
N=$OPTARG
else
echo "Error: Unknown normalization method $OPTARG. Please choose from fn, swan, noob, illumina, raw or quantile."
echo "Error: Unknown normalization method $OPTARG. Please choose from fn, swan, noob, illumina, raw, quantile or qn.bmiq."
exit 1
fi
;;
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