From dee3c17b7fece7850818df6efcba9de24e6c193e Mon Sep 17 00:00:00 2001 From: Jens Preussner Date: Wed, 31 Aug 2016 11:53:42 +0200 Subject: [PATCH] Allowed qn.bmiq and added help --- src/admire | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/admire b/src/admire index c402443..c48e8f4 100755 --- a/src/admire +++ b/src/admire @@ -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 @@ -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 ;;