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 …
deseq2 full and reduced model interpretation
2022年5月30日 · Most people are interested in specific comparisons when performing differential expression analyses with DESeq2. These comparisons are usually like do males have higher …
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 …
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 …
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 …
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 …
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 …
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. …
DEseq2 contrast in two time points - Bioinformatics Stack Exchange
2021年10月8日 · Deseq2 model formula and longitudinal experimatal (or time-series) designs Hot Network Questions When choosing between competing metaphysical theories to determine …
rna seq - Highly variable genes analysis by DESeq2
2018年4月13日 · deseq2; or ask your own question. Featured on Meta We’re (finally!) going to the cloud! More network ...