RawIntensity values identical to ImputedIntensity

[bolak92]

Hello,

During a recent data analysis, I observed that the RawIntensity values in the exported amica file are identical to the ImputedIntensity values. This occurred after a run with vsn normalization and no imputation.

Steps to Reproduce:

1. Conduct a run with vsn normalization.
2. Ensure no imputation is selected.
3. Export the amica file.
4. Inspect the values of RawIntensity and ImputedIntensity.

I suspect this behavior might be a bug. Would you be able to provide clarification or confirm the issue?

Kind Regards, Bola

[bolak92]

I am suspecting that this happens around line 293 if file runAnalysis.R that the cols RawIntensity gets replaced by ImputedIntensity in place.

[tbaccata]

Hey Bola,

I'm assuming you have MaxQuant output?
Using amica's provided example data, that contains MQ's summed intensities (= raw intensities), LFQ intensities and iBAQ intensities, I could not reproduce this behavior.

All intensities differ after the analysis step.
In line 293 amica's imputed intensities are getting updated after (potential) normalization.

Best,
Sebastian