Changes between Version 5 and Version 6 of xQTLTutorialBiologistInspectingData

Timestamp:

2012-02-21T11:33:22+01:00 (12 years ago)

Author:

jvelde

Comment:

--

xQTLTutorialBiologistInspectingData

@@ -4 +4 @@
 
 So what was just uploaded? In the main menu, click on ''Browse data'' and then ''Investigation overview''. Click on the ''Refresh'' button. (this will re-query the database and provide the most up-to-date information. Also, for additional information about viewing data, see [wiki:xQTLBiologistBrowse])
+
+== Step 1: Getting an overview ==
 
 In the overview, you'll notice a distinction between ''Annotations'', ''Data matrices'' and ''Files''. This was added with your recent import`*` :
@@ -21 +23 @@
 * Clicking any red-squared Data matrix will take you to the ''Data matrices'' tab and set a filter on the ID of the matrix being displayed. The filters are sticky, but you can always remove them to resume normal browsing.
 
+== Step 2: Browsing a matrix ==
+
 Try browsing to the 'yeast_pheno_small' matrix, and pan around in the dataset using the controls on the top and left of the values. If you have R properly installed, try making a plot: click on ''Action'', ''Graph / heatmap with R'', select a resolution of 1680*1050, and click ''Plot full values''. (in the section ''Heatmap plot with clustering on'') Open the result by clicking on the thumbnail picture that appears. Expand the size of the popup if needed. Does the data look OK?
 
@@ -27 +31 @@
 When you are done inspecting:
 
-|| [wiki:xQTLTutorialBiologistUploadingData Previous: Uploading a new dataset] || [wiki:xQTLTutorialBiologistRunningAnalysis Continue to: Running a basic QTL analysis] ||
+|| [wiki:xQTLTutorialBiologistUploadingData Previous: Uploading a new dataset] <-- || --> [wiki:xQTLTutorialBiologistRunningAnalysis Continue to: Running a basic QTL analysis] ||
 
 `*` = A little information for more advanced users: under the hood, the R/qtl importer has tagged the geno- and phenotype matrices for use in QTL analysis. You can see this in the ''Configure analysis'' screen, view ''Datasets'', look at ''!DataNames'' 'genotypes' and 'phenotypes': these have ''!DataValues'' '!ClusterDemo_yeast_geno', crosslinking to 'yeast_geno', and '!ClusterDemo_yeast_pheno_small', crosslinking to 'yeast_pheno_small'. However, this tagging process has also been made easier: have a look at the ''Tag data'' tab, also in the ''Configure analysis'' screen.