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SVD on the entire 27k by 511 patients M value matrix, plot 1st eigenarray (u matrix) and "color" the points according to the dye with with each CpG was labeled:
M value: analysis of red probes, identification of adjustment variables
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PCs | Batch | Center | Day | Month | Year | Amount | Concentr. | Row | Column | Stage | Grade | Age |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | 0.999 | 0.9999 | 0.995 | 0.991 | 0.956 | 0.863 | 0.074 | 0.997 | 0.626 | 0.60 | 0.26 | 0.6206 |
Look at the outliers:
Weird!
Do one more test and remove the first eigengene together with the variables above:
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