Global loess normalization results

You can download this analysis as a little HTML website for documentation. If you are running MS Windows please make sure that the file is saved with the extension ".tgz". For some reason Windows seems to want to rename the extension to ".gz" so it won't be unpacked correctly.

Here your will find the results of the normalization process. Hover with your mouse over the the images. When it is over a dot, the name of the gene will appear in a tooltip window.

Scatterplot

The image below shows a scatterplot of your data before normalization.

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The image below shows a scatterplot of your data after normalization. The cloud of points should now be centered around the dashed red line.


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See these two images switch on mouseover!

MA-Plot

The MA-Plot is a plot of the logarithms of the intensities ( A := 1/2 * ( log(R) + log(G) ) ) against the logarithms of the ratios of the intensities ( M := log(R) - log(G) ).

The green line is the loess regression curve.


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The MA-Plot after the normalization should be centered around the red dashed line and the loess regression curve should lie on the red line.


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See these two images switch on mouseover!

Data

The results of the normalization can be imported into excel easily. You can copy and pasted the data from the textarea below into an excel worksheet. To do this, click into the textarea. Push [Ctrl+A] to mark everything, then push [Ctrl+C] to copy it to your clipboard. Click on a field in your excel worksheet, then push [Ctrl+V] to insert the data.

Or download the result as an excelfile.

The meaning of the columns:
gene The name of the gene as given in the input.
Red The intensity value for the red channel
Green The intensity value for the green channel
Red_normalized The normalized red intensity
Green_normalized The normalized green intensity
M log( Red/Green )/log(2), that is the log-ratio to the basis of 2.
A log( Red*Green )/(2*log(2)), that is the log-intensity of the spot.
N log( Red_normalized/Green_normalized )/log(2), that is the normalized log-ratio to the basis of 2
normalized_ratio 2^N or, in other words, the normalized ratio