[BioC] saturated spots

[Hans-Ulrich Klein]

Dear all,

I currently analyse some selfmade oligo chips. The green channel 
contains the results of a ChIP-experiment. The red one contains genomic 
DNA. I read in the data and did some quality plots using limma. 
Unfortunatly, most arrays show strong saturation effects.

Some plots for interested readers:
MA-plot: http://img402.imageshack.us/img402/6323/maplotqa1.png
density: http://img146.imageshack.us/img146/482/densitynotlogjo9.png
density log2: http://img183.imageshack.us/img183/9416/densitylogmt8.png

It is certainly not a good idea to ignore the saturation. The saturated 
spots are not flagged by the image analysis software. (Only non-flagged 
spots are plotted in the images above.) My solution is to set a 
threshold value for each array manually just before the saturation peak 
(using the density plots) and then flag all spots with intensities 
larger than the threshold. The flagged spots are not used for 
normalization and further analysis.

Are there any R-packages dealing with saturation problems? Maybe for 
detecting the threshold automatically or for correcting saturated spots 
with non-linear transformations. I have found none.

How do you handle such saturation effects in your data?

Thank you very much for any suggestions,
Hans-Ulrich

-- 
Westfälische Wilhelms-Universität Münster
Department of Medical Informatics and Biomathematics
Hans-Ulrich Klein, Domagkstr. 9, Raum 27, 48149 Münster