Changes between Version 2 and Version 3 of SOP/MassSpec


Ignore:
Timestamp:
12/06/24 11:15:44 (7 months ago)
Author:
gbell
Comment:

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  • SOP/MassSpec

    v2 v3  
    4040 
    4141    * To identify differentially expressed proteins, use the normalized Total Spectrum Count
    42       * Recommended statistic: t-test on log2 transformed values
     42      * Normalize across samples (typically using quantile normalization)
     43      * Impute missing value (typically with the half-minimum method, which imputes any missing values for a protein with half of the minimum assayed value for that protein)
     44      * Recommended statistic: t-test or moderated t-test (such as is implemented in 'limma') on log2 transformed values
    4345      * Correct p-values with FDR (or an alternate method)
    4446