Coherence Control
Previous  Next



This section allows the user to check the Plates (either one by one or all together) to look for non-concordant repetitions.

Remember that SNPator won't allow you to Transfer  data to the Genotypes table if contradictory results remain in the Raw Genotypes table. Thus, it is very important to use this section to clean up contradictions before transferring your data.

The form looks like this:



graphic

You can select which plate you want to work with using the combo box on your left:


graphic

Selecting All Plates it is possible to find all contradictions in the study. Selecting a particular Plate, on the other hand, only will show intraplate contradictions but will miss contradictions between different Plates.

The Show All option in the center allows you to view all results that have been canceled in case you wanted to reevaluate them.

The Add Report option will create a report in a text file containing all the coherence control information. The Report will be added in the User Results section.

The Report Only option will run in background and will create the coherence control report in the User Results section but no information will be interactively shown on the screen. For efficiency purposes, the maximum amount of errors which is allowed to be shown on screen is limited to 500.

Click the Go button, wait for a moment and you get the list of contradictions:

graphic

This screen shows the list of Genotypes for which contradictions have been detected (they were also given to you in the Plate Report). They are classified into 3 categories:

Errors:

Genotypes that present contradictions other than the homozygous - hemizygous pair (i.e A/AA, G/GG etc...)

Example: AA/AT

     Data Transfer will be not allowed in any case when errors are present.

Warnings

Genotypes that present contradictions of the homozygous- hemizygous type.

Example: A/AA

When warnings are present, the user will be given the option of performing a Data Transfer.

Notices

Any kind of incoherences (Errors or Warnings) including only genotypes that have been canceled by the user.


To see them, that is, to see the particular results that happen to be non- concordant, you must click the Modify option and a new window appears:


graphic


In this window, one or more Genotypes can be canceled by the user. You can only cancel those results you have introduced yourself (That is, the "user" field has to match the current user. This is important. In case several users are uploading results in the same Study it avoids them messing with each others data). By default, Canceled Genotypes will not be taken into account when performing a coherence test (except when they generate Notices).

When the point has been reached in which there is a single result for every Genotype (no matter how many times this result may be repeated), data will be ready to be transferred to the Genotypes table, so that Analysis procedures may begin.

graphic