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--- how_to:studio:viewxic [2015/04/03 09:54]
132.168.72.237 [Display Protein Sets]
+++ how_to:studio:viewxic [2015/12/15 10:58] (current)
132.168.72.206
@@ Line 3: / Line 3: @@
 To display a XIC, right click on the selected XIC node in the Quantitation tree, and select "Display Abundances", and then the level you want to display:
-{{:how_to:studio:xic_display_popup.png|}}
+{{:how_to:studio:displayxicpopup.png|}}
 ==== Display Protein Sets ====
@@ Line 15: / Line 14: @@
 {{:how_to:studio:xic_display_proteinset.png?700|}}
-The overview is based on the abundances values.
+The overview is based by default on the abundances values.
+(Note: if you sort on the overview column, the sort is based on max(value-mean(values))/mean(values).
+So, you will obtain the most homogenous and confident rows first)
 For each quantitation channel, are displayed:
@@ Line 38: / Line 39: @@
 === Peptides ===
-A graph allows you to see the variations of the abundance (or raw abundance) of a peptide in the different quantitations channels:
+A graph allows you to see the variations of the abundance (or raw abundance) of a peptide in the different quantitation channels:
 {{:how_to:studio:xic_display_peptide_graph.png?|}}
@@ Line 49: / Line 50: @@
 By clicking on {{:how_to:studio:chart-arrow.png?|}} you can display either:
-- the peaks of isostope 0 in all quantitations channels
+- the peaks of isostope 0 in all quantitation channels
 - all isotopes for the selected quantitation channel:
@@ Line 55: / Line 56: @@
 {{:how_to:studio:xic_isotopes.png?|}}
-By clicking on {{:how_to:studio:wave.png?|}} you can see the chromatograms of the features and their first time scan and last time scan in mzScope. For more details see the mzScope section [[how_to:studio:mzscope]].
+By clicking on {{:how_to:studio:wave.png?|}} you can see the chromatograms of the features and their first time scan and last time scan in mzScope. For more details see the [[how_to:studio:mzscope|mzScope section]].
-==== Display peptides ====
+==== Display Peptides ====
 By clicking on “Display Abundances" / "Peptides”, you can see:
@@ Line 76: / Line 77: @@
 {{:how_to:studio:xic_display_peptideions.png?|}}
+==== Display Experimental Design and Parameters  ====
+By clicking on "Exp. Design > Parameters", you can see the experimental design and the parameters of the selected XIC.
+{{:how_to:studio:displayxicdesign.png|}}
+{{:how_to:studio:displayxicparam.png|}}
+If you have launched the refinement of the protein sets abundances on the XIC, you can also display the refinement parameters.
+==== Display Map Alignment ====
+By clicking on "Exp. Design > Map Alignment", you can see the map of the variation of the alignement of the maps compared to the map alignment of the selected XIC. You can also calculate the predicted time in a map from an elution time in another map.
+{{:how_to:studio:displaymapalignment.png|}}

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