Question: Is there a fair way to compare beta values from Sleuth output to the log Fold changes from EdgeR?
gravatar for cristina.osuna.cruz
2.4 years ago by
cristina.osuna.cruz10 wrote:

Dear all,

I am trying to do a fair comparison of the Differential expression results that I have obtained using two different approaches, one using Sleuth pipeline and the second one using EgdeR. However, I realized that Sleuth reports beta values instead of the worldwide used log Fold changes, which complicates a bit the comparison. In Sleuth documentation, they refer to the'beta' values as the effect size, 'technically a biased estimator of the fold change'. However, I have read it is not exactly the same and they should NOT be directly compared...

I have tried to compute from scratch my own log Fold change values from the normalized counts, but I do not get exactly the same results as EdgeR, apparently, the reason why this is happening is because edgeR does not simply take the averages of individual cpm values (, it is also taken into account other parameters such as the library size or the size of the counts...

Any ideas or suggestion to solve it?

Thank you in advance,


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