Analysis of microarray data - VSN International

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60Analysis of Microarray Data in GenStatThe spatial variation across the slides can be examinedby selecting the Spatial Plot item from the Explore submenu.The menu (right) shows the settings that can beused to produce a spatial plot for each slide. The spatialplot of the first slide is shown below.Dye intensity and spatial effects (pins, rows and columns) can be removed from the slides by using theNormalization menu. To open the normalization menu select Two Channel from the Normalize item onthe Microarrays menu. The menu below shows the settings that can be used to normalize the data.Note that the option to include plots is available within the options for this menu. You will need to openthe options dialog with Options button and set this as below right:
The resulting graphs display the effects that have been estimated:Analysis of Microarray Data in GenStat 61
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Analysis of microarray data - VSN International

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