Are signal values of different ChIP-seq experiments from ENCODE project comparable?

Question

[Ruijiang HAN]

I am a newbie. I recently started using TF ChIP-seq, using the narrow peak data of the ENCODE project. I want to know if signal values from different ChIP-seq experiments are comparable? Or the signal value is influenced by the number of cells, sequencing depth or anything else?

[ATpoint]

What is a signal value, from which files do they come, please add some background, best would be a link that is representative.

[Ruijiang HAN]

narrow peak format http://genome.ucsc.edu/FAQ/FAQformat.html#format12 ENCODE TF ChIP-seq https://www.encodeproject.org/chip-seq/transcription_factor/

Answer 1

[benformatics]

Signal value (assuming you mean peak "intensity") will not be quantitatively comparable between experiments. Everything you mention has the potential to affect the results. Another big factor however will be that two different people in two different places with different reagents will have done the same experiment. There are a huge number of variables you can't control.

You might try to compare ratios of signals within an experiment like Experiment 1: Hox1/ActinA signal ratio vs. Experiment 2: Hox1/ActinA signal ratio.

[Ruijiang HAN]

Thank you for your answer, it is very useful to me 🐎

[benformatics]

I mean you could qualitatively compare signals... like "I see a strong signal at gene X in experiment A and experiment B" but I wouldn't use it for anything more than guiding future questions/experiments or seeing whether a given result was reproducible. Essentially you can compare them; but I would never treat them as replicates.