Deseq2 batch effect. My question is, how would we interpret differences in basemean between genes, pertaining to reliability and su Sep 22, 2023 · I am trying to calculate log2FoldChange in DESeq2 by hand because I am trying to reproduce my results and understand how DESeq2 works. Mar 22, 2021 · I obtained a matrix of RNA-seq count data that has been normalized by DESeq2's median of ratio method. I know that DESeq2 wants to take in un-normalized counts, but I do not have access to those da Understanding DESeq2 design, contrast and results Ask Question Asked 8 years, 4 months ago Modified 8 years, 3 months ago Dec 30, 2021 · The basemean is described as the "mean of normalized counts of all samples". Members here do experience of DESEQ2 for transformation (I don't) and whilst the information could be enough, it is etiquette to provide as much detail as you can. Sep 17, 2021 · And I noticed that DEG analysis tools such as DESeq2/edgeR/etc cannot be applied for data with no replicates. Is there anything I can try for the analysis? Aug 11, 2021 · Adjusted P-value from DESeq2 Ask Question Asked 4 years, 1 month ago Modified 4 years ago Feb 9, 2018 · Trying to use deseq2 for differential expression analysis (rna-seq) between three groups and also account for batch effect as the control were sequenced at a different time point. What I want to know is: Are the counts first fitted to a nega The results obtained by running the results command from DESeq2 contain a "baseMean" column, which I assume is the mean across samples of the normalized counts for a given gene. control: con sam Oct 31, 2020 · Hi @athanasia and thansk for your post. Understanding DESeq2 design, contrast and results Ask Question Asked 8 years, 4 months ago Modified 8 years, 3 months ago Dec 30, 2021 · The basemean is described as the "mean of normalized counts of all samples". For example, your data, size dimension, runs etc. wjk cafj bhlmnv ctnll6 kcqvns fqdrllm 8iv g5rzmp07 wklj trizme