how to interpret log fold change (log2FC) on two cases
Jan 13, 2022 · just quick bioinformatic question if possible. I did read few papers and could not understand what this log fold change means. to make it simple I have a log2 fold change (log2FC) …
r - About the log2 fold change - Bioinformatics Stack Exchange
Jan 13, 2022 · log(x/y) = log(x) - log(y) -> this is log math. Like @RezaRezaei says, the two calculations are the same. I guess there could be differences owing to how computers calculate the values.
r - Ranking metric in GSEA - Bioinformatics Stack Exchange
Jun 2, 2020 · I am using fgsea in r to calculate and plot a bunch of GSEA graphs. My question is whether it is acceptable to use the Wald statistic from DeSeq2 to rank the gene list? I have seen in …
I want to display the top 10 upregulated and downregulated genes in a ...
Aug 27, 2020 · You can get a dataframe with the top genes by making e.g. use of dplyr::top_n. Instead of the top 10 I used the top 3 for exmaple purposes. Also, don't know that much about genes so I …
Establishing Quantitative Links Between Regulatory Activity Marker ...
Oct 15, 2024 · I am working on correlating H3K27ac ChIP-seq data, which indicates gene expression-related activity in regulatory regions, with RNA-seq gene expression data to establish quantitative …
r - Detecting differentially expressed genes with foldchange >= 2 and ...
Jun 21, 2018 · I'm using edgeR for differential analysis. Using glmTreat function I'm detecting differentially expressed genes between Tumor and Normal. I have set the arguments like below: tr …
Determine expression values for a defined list of genes across ...
Feb 23, 2023 · Please clarify more precisely what you want, as there is inconsistency in your question. log2FC values are log-transformed fold change values, and represent a change between two …
Is there an R function to plot a single variable as a heatmap?
Sep 16, 2020 · I've generated some RNA-seq data and have my list of DE genes between two groups and fold-changes (log2FC). I'd like to be able to plot a summary heatmap of log2FC for this group …
Creating a boxplot showing the spread of gene-expression within ...
Dec 10, 2022 · Thank you! The graph still looks a bit messy though..since there's so many bars they looked squished together with little space in between. Do you know if there's a way to put the 10 …
r - How to check if value is above threshold for each row, but the ...
Jul 16, 2021 · I have a df with 7 columns, the first 6 are log2FC values for gene expression, the 7th contains the name of the column with the highest log2FC value for each gene. I'm trying to create a …