Oct 11, 2018 · Biostats programs will often estimate log2 (condition1) using mean (log2 (condition1)). This is equivalent to taking the geometric mean of the original data. Thus, Log2FC = mean (log2 (condition1)) - mean (log2 (condition2)) is the same as Log2FC = log2 (geo_mean (condition1)/geo_mean (condition2)).

Mar 5, 2024 · log2(mean(exp(cluster_B_norm_data)-1) + 1) - log2(mean(exp(other_cluster_norm_data)-1) + 1) #> [1] 1.241319. The logFC is very different. The pseudo-count can have a large effect when the counts are small.

Jun 14, 2024 · Another interesting plot is the MA-plot (“Mean-Average” plot), a scatter plot of log2FC versus the mean of normalised counts. Genes with a padjusted value lower than 0.05 are colored.

Jan 13, 2022 · 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) value 2 between condition A and B. Does it mean A is two times higher compared to B or A is two times smaller compared to B?

If I calculate log2(B.Mean/A.Mean) For most of the genes the values are close to log2FC which calculated by Deseq2 but for "TNMD" the value is very different ! "log2FC = 0.71236 , "log2FC = 0.71236 , my log2foldchange = 3.964"

May 19, 2024 · The log2 fold change (log2FC) term is commonly used in bioinformatics to measure the changes in gene expression between two conditions (e.g. control vs. treated). log2 fold change is the ratio of expression levels between two conditions and it is calculated by taking log2 of the ratio of expression levels of two conditions.

Jul 5, 2020 · I have RNA-seq data (3 replicates for 2 different treatments) from a bacterial genome and have used DeSeq2 to calculate the log2fc for genes (padj < 0.05). This generates a csv file that includes (but is not limited to) the gene name and the log2fc example of output.

Nov 9, 2020 · Longer genes tend to have higher CPM values than shorter genes. But that is ok, as in RNA-Seq experiments, we do not compare between genes, only compare the same gene between different samples. 1. For each gene, calculate geometric mean. Gene 2 ...... Gene n. 2. For each gene, calculate ratio to geometric mean. Gene 2 ...... 3.

Nov 11, 2021 · Using log2 value become particularly helpful for visualising the gene expression changes. Furthermore, it eventually become intuitive that log2FC of 1 means expression level double in a given condition, and a negative log2FC means the gene is …

For one gene, I would calculate its log2FC as the logarithm(2) of the ratio between the mean of normalized counts in treated samples and the mean of normalized counts in control samples. But, if I do this operation manually, the result is not the same as the EdgeR one.