Dear ResearchGate community,
I am currently conducting SILAC data analysis using the Perseus program. My aim is to obtain a list of proteins with significant and high H/L ratios. However, I have encountered an issue with my protein list obtained from MaxQuant, where some signals were not detected, leading to the inability to calculate the ratios.
To address this issue, I have tried using the imputation feature in Perseus, but found that the intensity values were imputed based on the normalized ratio, rather than at the intensity level, resulting in the loss of some important ratios.
I would greatly appreciate any guidance or suggestions on how to overcome this issue and obtain a reliable list of proteins with significant and high H/L ratios.
Thank you in advance for your help and advice.
Sincerely,
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