I am using Agilent two color arrays and the experimental design included a dye-flip between arrays.
The agilent feature extraction output file do nicely load into MeV (unsing the Agilent file loading dialog). However, clustering is then difficult since the control experiment is in one array in the Cy3 channel, in the other dye flip experiment in the Cy5 channel.
I tried to solve that problem of the "two-color-array" by indication each single array what to use as the control and what to use as the experiment. But I could not find such specifications.
As an alternative, I tried to load the Agilent files as single-color experiments and to indicate which of the dataset are controls and which are experiments. But the Agilent files do not load as single-color-experiments.
Is there any sugesstion how to proceed?
Would it be an alternative to assemble all rProcessed and gProcessed data of the agilent arrays in a new table and to load them by TDMS files? Do I loose important information from the original Agilent files, or is additional information not used anyway?
Thanks for any suggestion!