Differences

This shows you the differences between two versions of the page.

--- how_to:studio:datamixer [2016/07/01 14:45]
132.168.72.206
+++ how_to:studio:datamixer [2016/07/04 11:50] (current)
132.168.72.206
@@ 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 52: / Line 59: @@
 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 ====
@@ Line 63: / Line 78: @@
 ==== missing values filter Function ====
-This function is used for ProStar Macro to remove rows with too many missing quantitative values
+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

Proline

User Tools

Site Tools

Differences

Page Tools