Changes between Version 1 and Version 2 of xQTLTutorialBiologistBrowsingResults

Timestamp:

2012-02-21T11:40:57+01:00 (13 years ago)

Author:

jvelde

Comment:

--

xQTLTutorialBiologistBrowsingResults

@@ -5 +5 @@
 After clicking the link in the ''Output'' column in the previous part of the tutorial, you are taken to the results of the analysis. You'll nice that browsing the results takes place in the same data matrix viewer as mentioned before in the tutorial at [wiki:xQTLTutorialBiologistInspectingData] and in the general manual at [wiki:xQTLBiologistBrowse]. Here we will discuss a few things specific for looking at QTL profile results.
 
+== Step 1: Fix annotation ==
+
 The first thing to notice is that the columns are typed as '!DerivedTrait'. The QTL analysis tool is not aware what specific type of trait is processed, so it uploads the results as '!DerivedTrait'. This type is normally used for a trait constructed during analysis, for example how one could construct a !DerivedTrait called 'BMI' using Measurements 'Weight' and 'Length'. In any case, the source data were probes, so let's change this to Probe.
 
@@ -10 +12 @@
 
 Notice that the probe name ("A_06_P4350", "A_06_P7031", etc) turn from black to blue. This means the data matrix is now matched to the annotations. You can hover over these names to see more information, or click on them to immediatly browse to that record in the database in the ''Annotations'' menu.
+
+== Step 2: Filter and download QTLs ==
 
 Let's find the probes with very significant QTLs. You can filter the matrix to do this. In the matrix viewer, click on ''Action'', then tick ''RC Filter on two dimensions''. (in the ''Special'' column) Now fill in the filter: ''Select all probes with at least '''1''' marker(s) having a value '''greater than 10'''''. Click ''Apply to all''.
@@ -23 +27 @@
 Now, try using the two-dimensional filter to zoom further into the data. Select only those markers with at least 1 probe with a LOD score of > 5. Remember to click on ''Apply to visible''. Try to create the same type of heatmap plot as before. Is this plot more useful?
 
+== Step 3: Filter and store as new matrix ==
+
 Let's take a different viewpoint on the data. Press the ''Reset'' button. This will restore the matrix to its original, unfiltered state. We will filter the markers on their chromosome annotation. Click ''Action'', under ''Filter on attributes:'' tick ''markers''. Now set the filter as follows: '''Chromosome_name''', '''equals exactly''', '''chr15'''. Click ''Apply to all''.
 
@@ -33 +39 @@
 Your data selection is now stored as a new matrix. Notice that the annotions are wrong, which you can fix by now. In addition you probably will want to explain something about this piece of data, using the ''Description'' field of the new matrix entry. (use ''Show additional fields'')
 
-|| [wiki:xQTLTutorialBiologistRunningAnalysis Previous: Running a basic QTL analysis] ||
+|| <-- [wiki:xQTLTutorialBiologistRunningAnalysis Previous: Running a basic QTL analysis] ||