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update imputation page
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hsiaoyi0504 committed Nov 11, 2024
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# Missing value imputation options

Multiple imputation options were provided in FragPipe-Analyst
Multiple imputation options were provided in FragPipe-Analyst. Perseus-style ** is applied by default for DDA and DIA LFQ data. No imputation is performed for TMT data by default.

- **Perseus-type:** This method is based on popular missing value
imputation procedure implemented in *Perseus* software by MaxQuant
team. The missing values are replaced by random numbers drawn from a
normal distribution of *1.8* standard deviation down shift and with a
width of *0.3* of each sample.
- **bpca:** Bayesian missing value imputation
- **knn:** Missing values replace by nearest neighbor averaging
technique
- **min:** Replaces the missing values by the smallest non-missing
value in the data.
- **Perseus-style**: This method is based on popular missing value imputation procedure implemented in *Perseus* software by MaxQuant team. The missing values are replaced by random numbers drawn from a normal distribution of *1.8* standard deviation down shift and with a width of *0.3* of each sample.
- **knn:** Missing values replace by nearest neighbor averaging technique
- **min:** Replaces the missing values by the smallest non-missing value in the data.
- **zero:** Replaces the missing values by **0**.

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