Fold Change Calculation Related Issues #65
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Dear fragpipe-analyst developers, I have questions about the fold change in the DE_results.csv file obtained after the software does or does not use the VSN or median centering method. I would like to understand the correlation between the values in the Imputed_matrix.csv file and the fold change. I am working with DIA data, and I wonder if the fold change (FC) is calculated using the raw quantification values from the report.pg_matrix.tsv file output by DIANN when no normalization method is specified, as I found that this corresponds with the DE_results.csv file. However, I have other questions, such as why different normalization methods result in different FCs in the DE_results. Could you please tell me the general data processing steps of fragpipe-analyst? Thank you very much! ctuo |
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Replies: 1 comment
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Duplicated as #66. |
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Duplicated as #66.