Baseline & OD

[Simina Pitur]

Hello! 

I have a question regarding baseline values and converting to OD.

From the formal definition of ΔOD, I understand it’s a function of light intensity during rest (baseline) / intensity during test (see attached screenshot). However, looking into hmrIntensity2OD, the actual function seems to use the average of test values as rest (see attached screenshot).

I first wanted to check whether I understand this correctly.

But I also wondered whether someone has chosen, for their own data preprocessing, to modify the function so that it uses the average of the actual recorded baseline. 

Thank you,

Simina

[Boas, David]

Taking the average of the whole time course versus taking the average of only the baseline periods for calculating OD will only cause a baseline shift in the OD values. We correct for these baseline shifts during the GLM function which subtracts off the baseline period from the results. You can go ahead and proceed with the idea you have, but it will make no difference in the final results.

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