Binarization threshold

[pvtodorov]

Hi!

Really cool package that's easy to use. I've already compared it to some prior selections using geneBasis and think I'd like to switch over. One of the things I'm I'd like to make sure I understand is how the binarization thresholds are set. In the "Expression quantization" section, you recommend using a threshold matching approach, where a threshold value of zero is used in the scRNA-seq measurements. You then suggest finding the corresponding quantile in the scRNA-seq data and identifying the matching threshold in the FISH data.

I'm starting from scRNA-seq data available and plan to select a 100-gene panel for smFISH data. I was wondering if the following an appropriate procedure:

1. Preprocess the scRNA-seq data, including quality control and filtering steps.
2. Normalize and transform the scRNA-seq data using an appropriate method such as log CPM or SCTransform.
3. Set the threshold value to 0 for the transformed scRNA-seq data.

All the best, Petar

[iancovert]

Hi Petar,

Thanks for checking out the package, and I'm glad you're finding it easy to use! As for the binarization threshold, like you said, the idea is to set the threshold to zero for the scRNA-seq data and then find a corresponding threshold in the FISH data once it's collected. So the three steps you've described on the scRNA-seq side sound like a correct procedure to me.

Let me know if there's anything else I can help figure out.

Ian