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--- how_to:studio:datamixer [2015/06/30 10:01]
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+++ how_to:studio:datamixer [2016/07/04 11:50] (current)
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@@ Line 1: / Line 1: @@
-====== Data Mixer ======
+====== Data Analyzer ======
-The purpose of the Data Mixer is to easily do calculations/comparisons on data.
+The purpose of the Data Analyzer is to easily do calculations/comparisons on data.
-To open the data mixer, you have two possibilities:
+To open the data analyzer, you have two possibilities:
-- you can use the dedicated button that you can find in the toolbar of all views. If you use this button, the corresponding data is directly sent to the data mixer
+- you can use the dedicated button that you can find in the toolbar of all views. If you use this button, the corresponding data is directly sent to the data analyzer.
 {{:how_to:studio:startdatamixer.png}}
-- you can use the menu "Window>Data Mixer"
+- you can use the menu "Window>Data Analyzer"
-{{:how_to:studio:menuDataMixer.png}}
+{{:how_to:studio:menudataanalyzer.png}}
-In the Data Mixer view, you can access to all data views, to some functions and graphics. In the following example, we create a graph by adding by Drag & Drop the Spectral Count Data and the BBinomial function. Then we link them together.
+In the Data Analyzer view, you can access to all data views, to some functions and graphics. In the following example, we create a graph by adding by Drag & Drop the Spectral Count Data and the BBinomial function. Then we link them together.
 {{:how_to:studio:dataMixerV2.png}}
@@ Line 35: / Line 35: @@
 ===== 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 ====
@@ Line 45: / Line 52: @@
 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 usefull for XIC Quantitations
+Calibration Plot for Proteomics is discribed here : https://cran.r-project.org/web/packages/cp4p/index.html
 ==== bbinomial Function ====
-bbinomial function is usefull for Spectral Count Quantitations
+bbinomial function is useful for Spectral Count Quantitations
+==== diff analysis Function ====
+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|}}
+: Add XIC Data to Data Analyzer from the Protein Set View.
+: Add Prostar Macro by a drag and drop and link XIC Data to the Macro
+: Process the Graph by clicking on the button
+During the process, the Data Analyzer will ask you settings for each function.
+: Filter is needed only if you want to remove contaminants. Settings can be
+validated with no parameters if you don't need it.
+: Log is needed to log abundances (Data from Proline). For Data coming from Max Quant, data
+is already logged.
+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

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