Handling Negative Values in Log-Transformed a Dataset for Differential Expression Analysis with Limma

Question

[Maryam]

Hi everyone!

I am analyzing dataset GSE49515 and have obtained the preprocessed series matrix, which contains normalized, log-transformed values.

However, I have noticed the presence of negative values in this matrix, and I am unsure if these negative values are a result of background correction or log transformation. Unfortunately, I am unable to analyze the CEL files.

Can I proceed with these negative values for the purpose of performing differential expression analysis using Limma? If not, should I replace the negative values with zero or NA? Or can I add the minimum value to all values? Or if you know another better way I appreciate if you tell me.

Answer 1

[Gordon Smyth]

There is no problem with negative values on the log-scale. limma can handle them perfectly well. You don't need to take any special action.