I use the SpotPix Suite to load my ABI-array files and do the filtration just like it's described in the Magma-guide. When i change the order of the filtration routine (remove spots with flags > 8191 before s_n < 3.0) i get a whole different set of genes. Why is that? Shouldn't these routines be independent of each other?

I load 3 replicas from 6 different time points, use time point 1 as the base sample and use "signal" as input and "log vs base" as the output. The "Quantile Normalize All Arrays" box is checked

When I compile an ABI-result file I get the following message:
"Encountered Error and halted
Error:
java.lang.ArrayIndexOutOfBoundsException: 3"

I can't fine anything wrong with just looking at the file. What may be the problem?

Hans-Richard

Thank you,
but doesn't this box relate to the "Combine in-array replicate"-box, meaning replicate spots on the same array? Or does it combine values from replicate arrays/samples? Or both?

Hans-Richard

When adding replicate data sets in the SpotPix Suite, how are the final signal intensities/log ratios calculated. As far as I can see they differ from the average.

Thanks a lot
Hans-Richard