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tbaccata / amica

amica: an interactive and user-friendly web-based platform for the analysis of proteomics data
GNU General Public License v3.0
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`RawIntensity` values identical to `ImputedIntensity` #28

Closed bolak92 closed 1 year ago

bolak92 commented 1 year ago

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 commented 1 year ago

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

tbaccata commented 1 year ago

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