This is my example of dataframe (this is just a sample for testing the formulas):
dhBMEC_1 dhBMEC_2 dhBMEC_3 cryo.dhBMEC_1 cryo.dhBMEC_2 cryo.dhBMEC_3 iPSC_1 iPSC_2 iPSC_3 653635 1217 689 1089 1200 1372 1099 729 661 657 102466751 16 5 16 8 24 25 1 1 4 729737 1281 1187 1188 1482 1379 1591 3056 2799 2268
I'm doing the calculations BY HAND of the 3 steps of the DESeq2:
- Estimate Size Factors
- Estimate Dispersions
- Negative Binomial GLM fitting and Wald statistics
For first step, I was using this page: https://github.com/hbctraining/DGE_workshop_salmon/blob/master/lessons/02_DGE_count_normalization.md Using that link, i was able to make the stimation of the size factors in only 4 steps.
That's what I need right now. An easy step by step of the algorithm. The problem is, I only have the information for the step 1 but now I need to make the same for the dispersion calculation and also is the hardest step. Could anyone help me with this?
The objective is to complete this formula:
I make a list of the Inputs that I need based in the previous ecuation (i don't know if it's ok). I put a ✔ on the items that I have now:
normalized counts ✔, dispersion ✔, vector de counts ✔, estimated coefficient vector ✘, matrix model X ✘ (or ✔, but idk what it is yet)
I'm extracting all the formulas from this links: