how_to:studio:datamixer
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how_to:studio:datamixer [2016/02/08 14:43] 132.168.72.206 |
how_to:studio:datamixer [2016/07/04 11:50] (current) 132.168.72.206 |
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| ===== Available Functions ===== | ===== Available Functions ===== | ||
| + | |||
| + | ==== compute FDR Function ==== | ||
| + | |||
| + | This function is used by ProStar Macro to compute the FDR. | ||
| + | |||
| + | More information: | ||
| + | http://bioconductor.org/packages/release/bioc/vignettes/Prostar/inst/doc/Prostar_UserManual.pdf | ||
| ==== join Function ==== | ==== join Function ==== | ||
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| When a key value is not found in one of the data source table, the line is displayed as empty. For numerical values a difference is done and for string values, the '<>' symbol is displayed when values are different. | When a key value is not found in one of the data source table, the line is displayed as empty. For numerical values a difference is done and for string values, the '<>' symbol is displayed when values are different. | ||
| - | ==== pvalue and ttd Functions ==== | + | ==== adjustp Function / calibration Plot ==== |
| - | pvalue and ttd functions are useful for XIC Quantitations | + | Calibration Plot for Proteomics is discribed here : https://cran.r-project.org/web/packages/cp4p/index.html |
| ==== bbinomial Function ==== | ==== bbinomial Function ==== | ||
| Line 53: | Line 60: | ||
| bbinomial function is useful for Spectral Count Quantitations | bbinomial function is useful for Spectral Count Quantitations | ||
| - | ==== adjustp Function / calibration Plot ==== | + | ==== diff analysis Function ==== |
| - | Calibration Plot for Proteomics is discribed here : https://cran.r-project.org/web/packages/cp4p/index.html | + | This function is used by ProStar Macro. |
| + | Two tests are available : Welch t-test and Limma t-test. | ||
| + | |||
| + | More information: | ||
| + | http://bioconductor.org/packages/release/bioc/vignettes/Prostar/inst/doc/Prostar_UserManual.pdf | ||
| + | |||
| + | ==== filter Function ==== | ||
| + | |||
| + | filter function let the user filter some rows of a matrix according to settings on columns | ||
| + | |||
| + | ==== import CSV/TSV ==== | ||
| + | |||
| + | This module lets you import data from a CSV or TSV file. Then you can do calculations and display these data directly in Proline Studio. | ||
| + | |||
| + | ==== missing values filter Function ==== | ||
| + | |||
| + | This function is used by ProStar Macro to remove rows with too many missing quantitative values. | ||
| + | |||
| + | The available missing values algorithm are: | ||
| + | * Whole Groups: The lines (across all groups) in the quantitative dataset which contain less non-missing value than a user-defined threshold are deleted. | ||
| + | * For every group: The lines for which each condition contain less non-missing value than a user-defined threshold are deleted. | ||
| + | * At least one group: The lines for which at least one condition contain less non-missing value than a user-defined threshold are deleted. | ||
| + | |||
| + | ==== missing values imputation Function ==== | ||
| + | |||
| + | This function is used by ProStar Macro to imput missing values. | ||
| + | |||
| + | More information: | ||
| + | http://bioconductor.org/packages/release/bioc/vignettes/Prostar/inst/doc/Prostar_UserManual.pdf | ||
| + | |||
| + | |||
| + | ==== normalize Function ==== | ||
| + | This function is used by ProStar Macro to normalize quantitative values. | ||
| + | |||
| + | More information on algorithms : http://bioconductor.org/packages/release/bioc/vignettes/Prostar/inst/doc/Prostar_UserManual.pdf | ||
| + | |||
| + | |||
| + | ==== pvalue and ttd Functions ==== | ||
| + | |||
| + | pvalue and ttd functions are useful for XIC Quantitations | ||
| + | |||
| + | |||
| + | ===== Prostar Macro ===== | ||
| + | |||
| + | {{:how_to:studio:prostarcheminement.png?800|}} | ||
| + | |||
| + | 1 : Add XIC Data to Data Analyzer from the Protein Set View. | ||
| + | |||
| + | 2 : Add Prostar Macro by a drag and drop and link XIC Data to the Macro | ||
| + | |||
| + | 3 : Process the Graph by clicking on the button | ||
| + | |||
| + | During the process, the Data Analyzer will ask you settings for each function. | ||
| + | |||
| + | 4 : Filter is needed only if you want to remove contaminants. Settings can be | ||
| + | validated with no parameters if you don't need it. | ||
| + | |||
| + | 5 : Log is needed to log abundances (Data from Proline). For Data coming from Max Quant, data | ||
| + | is already logged. | ||
| + | |||
| + | 6 to 12 : follow the settings asked ( you can find some help in Prostar documentation, or information in corresponding functions.) | ||
| + | |||
| + | During the process, results will be automatically displayed : calibration, scatter plot and FDR Result. | ||
| + | If you want to look at other results, right click on a function and select "Display in New Window" | ||
| + | Prostar User Manual : http://bioconductor.org/packages/release/bioc/vignettes/Prostar/inst/doc/Prostar_UserManual.pdf | ||
| + | Prostar Tutorial : | ||
| + | http://bioconductor.org/packages/release/bioc/vignettes/Prostar/inst/doc/Prostar_Tutorial.pdf | ||
| + | |||
how_to/studio/datamixer.1454938992.txt.gz · Last modified: 2016/02/08 14:43 by 132.168.72.206
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