Hello everyone, I am a beginner with the DESeq2 package, and I am trying to understand the mathematical principles behind this package.

In statistical modeling and hypothesis testing, a contrast vector c is used to construct specific linear combinations in order to test whether this linear combination equals a certain hypothesized value. A example below.

If I have a condition with four group, to avoid dummy trap & not full rank of matrix, a regression equation must like : Y = Beta_0 + Beta_1 * X_1 + Beta_2 * X_2 + Beta_3 * X_3 + error. Where "Y" is read counts and "Beta_1 to Beta_3" is dummy variables.

Question1: When I have a factor that has been incorporated into the intercept, and I want to compare Beta_1 with the factor that has been incorporated into the intercept, how should I set the contrast vector? Which one of the contrast vector ( [1,-1,0,0] or [0,1,0,0] ) is correct?

Question2: Log2foldChange represents the logarithmic expression difference between two groups. When the contrast vector multiply Beta vector = q. Is set to q = 0, doesn't taking the logarithm result in infinity? How does the software avoid the occurrence of infinite values?

Oh, and I don't understand your second question. If you set a contrast vector to be all zeros (which I think is what you are asking), then you are telling

`DESeq2`

that you don't want any comparison and it tells you that is not a thing.