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--- how_to:studio:datamixer [2016/02/08 14:30]
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+++ how_to:studio:datamixer [2016/07/04 11:50] (current)
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@@ Line 12: / Line 12: @@
 - you can use the menu "Window>Data Analyzer"
-{{:how_to:studio:menuDataMixer.png}}
+{{:how_to:studio:menudataanalyzer.png}}
 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.
@@ 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 useful for XIC Quantitations
+Calibration Plot for Proteomics is discribed here : https://cran.r-project.org/web/packages/cp4p/index.html
 ==== bbinomial Function ====
@@ Line 53: / Line 60: @@
 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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