Understanding DESeq2 design, contrast and results
It seems that the "combining factors" trick described in part 3.3 of DESeq2 current "vignette" (as of may 2017) under the title "Interaction" is a way to access to the desired contrasts. It seems …
How can I extract normalized read count values from DESeq2 …
DESeq2 offers two different methods to perform a more rigorous analysis: rlog — a regularised log, and; vst — a variance stabilising transformation. You’d generally use either of these for …
Use of "baseMean" in DeSEQ2 - Bioinformatics Stack Exchange
2021年12月30日 · I could write a long story about this but actually I will just link this excellent resource from HBCtraining which dissects the individual steps DESeq2 does, starting from …
Adjusted P-value from DESeq2 - Bioinformatics Stack Exchange
2021年8月11日 · An interpretation of the BH method for controlling the FDR is implemented in DESeq2 in which we rank the genes by p-value, then multiply each ranked p-value by m/rank. …
Install DESeq2 through anaconda - Bioinformatics Stack Exchange
Sounds like you might have an issue with which R Rstudio is running. If you didn't install Rstudio through conda, Rstudio may be using its own version of R that is bundled with Rstudio, instead …
how is log2foldchange calculated in DESeq2
2023年9月22日 · I am trying to do something similar where I have plot showing the differential expression results for a single gene from the DESeq2 output. I plotted the marplot of the …
rna seq - How does DESeq2 "collapseReplicates()" function work …
2022年1月18日 · $\begingroup$ I just realized reading the "Plot counts" section of the DESeq2 vignette that the function plotCounts "normalizes counts by the estimated size factors (or …
rna-seq bioconductor deseq2 - Bioinformatics Stack Exchange
2021年7月21日 · In DESeq2 you can identify your differentially expressed (DE) genes using the results function. I noticed people in my lab using the results() function with the minimum …
Newest 'deseq2' Questions - Bioinformatics Stack Exchange
I have different treatments (infected and control ones). When using DESeq2, I have different results in two ways of comparison. first way: factor: treatment, factor level1: Moribund Infected, …
DESeq2 multiple treatments, multiple time points, multiple cell lines
2021年5月4日 · Deseq2 model formula and longitudinal experimatal (or time-series) designs. Hot Network Questions Using ...