xQTL workbench - Tutorial for biologists: Inspecting your upload
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 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* :
Annotations:
- Individuals: the headers of the geno and pheno files you just uploaded, eg. "GSM238074", "GSM238122".
- Probes: the rows in the phenotype file, e.g. "A_06_P1038", "A_06_P7253"
- Markers: the rows in the genotype and map file, e.g. "YPL234C_2806", "YPL144W_2826"
- Chromosomes: automatically created from the chromosome numbers in your map file, if they didn't exist yet.
Data matrices:
- 'yeast_pheno_small': all of the data values of the phenotype file
- 'yeast_geno': all of the data values of the genotype file
You can click on any item to see the detailed view: the annotations will allow you to browse all records of that type, and the matrix view will let you browse the data values in two dimensions. Note that the links in Investigation overview are ofcourse just shorthands:
- Clicking any blue-squared Annotation will take you to the Annotation tab and select a type of annotation (Gene, Marker, Probe, etc)
- 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?
Go back to Investigation overview and now select 'yeast_geno'. Try to create the same plot as before. What happens? Select a resolution size of 800*600 and click on Plot full row. What information is shown in this plot? Now, use Plot full column. What information does this plot provide?
When you are done inspecting:
| Previous: Uploading a new dataset <-- | --> 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.
