Understanding DESeq2 design, contrast and results
Understanding DESeq2 design, contrast and results Ask Question Asked 8 years, 6 months ago Modified 8 years, 6 months ago
how is log2foldchange calculated in DESeq2
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. What I want to know is: Are the …
rna seq - Beginner with DESeq2 having issue with analysis ...
Jul 31, 2021 · Just load the output with the header, use rownames() to move the gene column to rownames, remove all the non-relevant columns (that is usually 1-7) and then feed the …
Use of "baseMean" in DeSEQ2 - Bioinformatics Stack Exchange
Dec 30, 2021 · The basemean is described as the "mean of normalized counts of all samples". My question is, how would we interpret differences in basemean between …
rna seq - Error in checkFullRank (modelMatrix) deseq2
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 …
Manually calculating log2 fold change values from DESeq2 …
Dec 29, 2022 · DESeq2 median of ratios nomalization seems to take care of that issue. So, I prefer using DESeq2 normalization. But I cannot use DESeq2 for getting log2 fold change …
DESeq2 multiple treatments, multiple time points, multiple cell …
May 4, 2021 · When comparing one subset of samples to another subset of samples, you generally do have to make a subset dds object. It's preferable to leave all the samples in for …
Adjusted P-value from DESeq2 - Bioinformatics Stack Exchange
Aug 11, 2021 · Adjusted P-value from DESeq2 Ask Question Asked 4 years, 3 months ago Modified 4 years, 2 months ago
How can I extract normalized read count values from DESeq2 …
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 …
Install DESeq2 through anaconda - Bioinformatics Stack Exchange
Install DESeq2 through anaconda Ask Question Asked 7 years ago Modified 5 years, 8 months ago