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I recently started using minfi for analyzing a large set of 450k methylation arrays. For a small trial run, everything worked as expected, but once you get over around 200 samples, there are some problems. Some functions like getBeta() work as expected. However, qcReport() and densityPlot() skip some samples. I don't get any errors. With density plots, it's hard to notice that any are missing, but with the bean plots, certain samples display the sample name, but the graph is blank. Changing the group labels changes which samples show up, so it's not a problem with the samples or the input object. Has anyone else run into this problem? Now I am concerned that other functions may be affected, but I am just not noticing it.
If the sample sheet is messed up, then subsetting it to problematic samples should produce problems again. However, if I subset the targets data frame to 20 samples that got skipped in a set of 200 and just use that, everything is fine.
I checked both Basename and sample name. Both of them only have unique values.