Contents
How do you find the p-value of a fold change?
You can’t calculate a p-value on the fold-change values, you need to use the concentrations in triplicate thus giving a measure of the variance for the t-test to use. t-test assumes your data are normally distributed, if they aren’t you’re going to get spurious p-values.
How do you calculate fold change in RNA-seq?
First, you have to divide the FPKM of the second value (of the second group) on the FPKM of the first value to get the Fold Change (FC). then, put the equation in Excel =Log(FC, 2) to get the log2 fold change value from FPKM value.
What fold change is significant in RNA-seq?
Statistical methods are used to select for the significant differential expression of genes in RNA-seq and microarray experiments but most previous study performed FDR (0.1, 0.05 and 0.01) and log2 fold change (1, 1.5 and 2) together.
How do you plot a fold change?
Fold change is calculated simply as the ratio of the difference between final value and the initial value over the original value. Thus, if the initial value is A and final value is B, the fold change is (B – A)/A or equivalently B/A – 1.
How are fold regulations calculated?
How do you interpret a log fold change?
It’s also useful to know that a log2 fold change (B/A) of 1 means B is twice as large as A, while log2fc of 2 means B is 4x as large as A. Conversely, -1 means A is twice as large as B, and -2 means A is 4x as large as B.
Can you calculate a p value on a fold change?
You can’t calculate a p-value on the fold-change values, you need to use the concentrations in triplicate thus giving a measure of the variance for the t-test to use. t-test assumes your data are normally distributed, if they aren’t you’re going to get spurious p-values. If you aren’t sure a non-parametric test like Wilcoxon is better.
What is fold change to consider in RNA-Seq?
Think about a protein that needs activation by phosphorylation. A small fold change, if it co-occur with the respective kinase, would have a much larger impact than a larger fold change when the kinase is not expressed.
Which is the correct fold change for Test status?
Fold change > 1.5, FDR < 0.05, P-value < 0.05 and ‘Test status’ = OK is one criteria which was taken, but I have also seen people considering fold change > 2. I took 3 replicates for the mutant and the wild type each.
How is the fold change of a group calculated?
Fold change is typically calculated by simply average of group 2/ average of group 1. I’ll give you a proof, in http://seqanswers.com/forums/showthread.php?t=49101, the author of DESeq2 wrote: The question is why would you want to do this? There are good Bioconductor packages that can do that for you.