Bioinformatics Toolbox

Statistics of the Microarrays

You can use the function maboxplot to look at the distribution of data in each of the blocks.

1. In the MATLAB Command Window, type

   figure
   subplot(2,1,1)
   maboxplot(pd,'F532 Median','title','Parkinson''s Disease Model Mouse')
   subplot(2,1,2)
   maboxplot(pd,'B532 Median','title','Parkinson''s Disease Model Mouse')
   figure
   subplot(2,1,1)
   maboxplot(wt,'F532 Median','title','Untreated Mouse')
   subplot(2,1,2)
   maboxplot(wt,'B532 Median','title','Untreated Mouse')
   

   MATLAB plots the images.

   

   

2. Compare the plots.

   From the box plots you can clearly see the spatial effects in the background intensities. Blocks numbers 1, 3, 5, and 7 are on the left side of the arrays, and numbers 2, 4, 6, and 8 are on the right side. The data must be normalized to remove this spatial bias.

Spatial Images of Microarray Data

Scatter Plots of Microarray Data

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