Jan 5, 2018 · if LogFC if 0.05, then your actual fold change is 1.0353... which is effectively 1, or rather, no significant change. To convert a logFC value, simply use it as the exponent of two: 2 logFC. In Excel, use the function "=2 x". To convert a FC value, take the log2. In Excel, use function: "=log(x,2). (where x = the cell with your data). Hope that ...

May 30, 2020 · If i take logFc > 1 , there is a significant number . But how can i say that those genes are differentially expressed, they can be in their normal range of expression. Just because I'm changing my cutoff from 1.5 to 1 it would mean something or it will be another mistake I'll be doing to consider them differentially expressed where in case they ...

Aug 26, 2023 · Increasing log2(?)-FC from 0.5 to 2 will diminish the number of genes, not increase. Most tend to go with logFC of 0.26-0.58 which represents a FC of 1.2 and 1.5 respectively. I personally go with 1.2 because a 20% change in expression could reasonably result in biologically meaningful effects.

May 18, 2022 · If you don’t have access to the code and someone else ran in it then you can try the following: use the normalized table, take the mean for each group to get 2 vectors, log2 transform the mean vectors, do disease - healthy, then plot the logfc values against what you just computed. They shouldn’t be exact but you should see a trend.

Jun 28, 2021 · This is available under lFC.Av, but under logFC, I get back another value. According to the test.results definition, it is the "log fold change estimated by fitting the given GLM model. The reference level of the main factor is taken as control".

Jan 5, 2018 · Posted by u/AnonBiomed - 5 votes and 7 comments

Jul 26, 2021 · The result is a list of differentially expressed genes and I am mainly looking at their LogFC for further processing. Now some genes have a positive LogFC (upregulated) or a negative LogFC (downregulated), but to which group do they belong (As in: in which group are they up- or downregulated compared to which group)?

Dec 1, 2021 · Hello, Previously when using fgsea I have ran it using genes based on a composite score: -log10(padj) * log2fc.

Jun 24, 2021 · “b UMAP embeddings of merged scRNA-seq profiles from resting and activated T cells from lung (LG), bone marrow (BM), and lung-draining lymph node (LN) in each of two organ donors colored by resting/activated condition, CD4/CD8 expression ratio (all cells in a given cluster assigned the same average value), and tissue source.”

Jun 22, 2024 · I am quite confused, I have another gene of interest which shows a logFc change of 1.1, p value= 0.004 , but p adj >0.05 before controlling for collection dates. After controlling the values pretty much remained the same. My supervisor wants me to stick to the former gene and continue downstream analysis on it because the p adj is significant.