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jonathangriffiths

barcodeswapping2017's Issues

Further fixes beyond my capabilities

  • Coefficient of determination is missing from Figure 9.
  • The text around Figure 20 says "This indicates that the expression abundance of sporadically expressed genes does not drive differences in the swapping fraction estimates." But you're looking at the information score, not the abundance (which you have previously shown to be poorly correlated with the information score).
  • Need more detail about "identical pools" in the last paragraph of Section 4.5; I am not sure what this means. Do you mean that one 2500 pool was used in place of the 4000 counts?
  • Cite SNN graph people (https://doi.org/10.1093/bioinformatics/btv088)
  • Notation for "Experiment 1" in Section 6.2.4 could be better. You're re-using Dataset 1, so call it Dataset 1a and Dataset 1b or something like that. You should also be explicit about how you're using these two libraries as a control for our method; are you trying to detect "swaps" between the two libraries?

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