diff --git a/README.md b/README.md index fea1179d40fc512f26dd161ceaca3e33fced7099..cd82346630cce06cd3917076296330e9afa45b9e 100644 --- a/README.md +++ b/README.md @@ -1,49 +1,13 @@ -# Counts simulations & DESEQ2 investigations +# DESEQ2 -Purpose: -1) Understand how DESEQ2 works <br/> -2) Understand how maximize statistical power <br/> -2) Refined biological protocol (seqeuncing effort, ...) <br/> +- [dispersion inference](results/v3/DESEQ2/2022_02_03_dispersion.html) +- [sequencing depth](results/v3/DESEQ2/2023_02_05_sequencingDepth.html) +- [replicates](results/v3/DESEQ2/2023_02_06_replicates.html) -## About DESEQ2 - -Main step: - -### 1) Estimate size factor - -Median ratio method is used to estimate the size factor per sample. - -The size factor is used for normalizing counts (per gene per sample). -Normalized counts allow minimizing biais linked to library size. -By normalizing the counts DESEQ2 aims to make sure differential expression are based on factors study and not to sequencing depth -/!\ gene length is not take into account ! - -### 2)Estimate dispersion - -Purpose: Estimate the variability between replicates <br/> - -Get dispersion estimate for each gene using Maximum Linkelihood Estimatation <br/> -Fit a curve to wise gene dispersion estimate - -### 3) Fit linear model - -The differential expression analysis uses a generalized linear model of the form: <br/> -Kij ∼ NB(µij , α i )<br/> -µij = s j q ij <br/> -log 2 (q ij ) = x j. β i <br/> - -where counts K ij for gene i, sample j are modeled using a Negative Binomial distribution with -fitted mean µ ij and a gene-specific dispersion parameter α i . The fitted mean is composed of a -sample-specific size factor s j and a parameter q ij proportional to the expected true concentration of fragments for sample j. The coefficients β i give the log2 fold changes for gene i for each column of the model matrix X. <br/> - -### 4) Wald Test: - -H0: Test if Log(FC) = 0 <br/> - -With DESeq2, the Wald test is the default used for hypothesis testing when comparing two groups. The Wald test is a test of hypothesis usually performed on parameters that have been estimated by maximum likelihood. The Wald test is also a standard way to extract a P value from a regression fit. - - -## HTRSIM +# GLM +- [dispersion inference](results/v3/GLM/2023_02_04_dispersion.html) +- [sequencing depth](results/v3/GLM/2023_02_05_sequencingDepth.html) +- [replicates](results/v3/GLM/2023_02_06_replicates.html)