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Normalisation

The position of the bands will not be the same on every gel. There are a number of reasons for this.

  • Experimental conditions may stretch one gel with respect to the other.
  • There may be local variations in migration rate.
  • The well may vary in location between gels.

In order to compare the bands from different gels is it necessary to map the band position on a particular gel to a standard gel. This mapping is calculated using the bands in the marker lanes and the set of standard bands defined in the standard file.

Given that the number of bands in a marker lane is the same as the number of standard bands then a mapping can be established between position in the marker lane and position on the standard gel. We can then extend this mapping to sample lanes by linear interpolation of the positions of the bands in neighbouring marker lanes. We now have a set of positions in each sample lane and the corresponding position on a standard gel. Note these positions correspond to the common set of bands in the marker lanes they do not necessarily correspond to bands in the sample lanes. This approach assumes each marker lane contains exactly as many bands as the standard lane pattern you may need to Edit the marker lanes to ensure this is the case.

If size information is available in the standard then Image will also calculate fragment size for each band.

The normalisation algorithm

refer to the relevant page on the web-site.

Last modified : November 1999 Image 3.10

* quick link - http://q.sanger.ac.uk/jlsm96y9