comparison msclust.xml @ 4:80075a4c6543

updated image paths

3:2c1c9f0d8aa6

  
This tool extracts spectra from ion-wise aligned MS(/MS) results. It uses expression profiles and 
retention times of the putative ions to cluster them. Each cluster is then used to generate 
one spectrum containing the clustered ions (peaks). 

.. image:: $PATH_TO_IMAGES/msclust_summary.png 


-----

**Output**

values = stricter separation at the value determined in 'Potential Density reduction' above  
(TODO review this comment). 

*Stop Criterion:* When to stop reducing and looking for new clusters. Lower values = more iterations 

.. __: javascript:window.open('$PATH_TO_IMAGES/confidence_and_slope_params_explain.png','popUpWindow','height=700,width=800,left=10,top=10,resizable=yes,scrollbars=yes,toolbar=yes,menubar=no,location=no,directories=no,status=yes')


-----

**Output files described below**

*SPECTRA:* this file can be submitted to NIST for identification of the spectra.

`Click here for more details on the Sample selection and Spectrum peak intensity correction algorithm parameters related to SPECTRA generation`_  

.. _Click here for more details on the Sample selection and Spectrum peak intensity correction algorithm parameters related to SPECTRA generation: javascript:window.open('$PATH_TO_IMAGES/sample_sel_and_peak_height_correction.png','popUpWindow','height=700,width=800,left=10,top=10,resizable=yes,scrollbars=yes,toolbar=yes,menubar=no,location=no,directories=no,status=yes')

-----

*MIC:* stands for Measured Ions Count -> it contains, for each cluster, the sum of the ion count 
values (corrected by their membership) for all MEASURED cluster ions in the given sample.

by the membership value of the peak in the cluster in case the SIM peak is "shared". If the SIM peak is not 
"shared" then the "raw" intensity values of the SIM peak are recorded in the SIM file. 

`Click here for more details on the SIM output file`_  

.. _Click here for more details on the SIM output file: javascript:window.open('$PATH_TO_IMAGES/sample_SIM.png','popUpWindow','height=700,width=800,left=10,top=10,resizable=yes,scrollbars=yes,toolbar=yes,menubar=no,location=no,directories=no,status=yes')



  </help>
</tool>

4:80075a4c6543

  
This tool extracts spectra from ion-wise aligned MS(/MS) results. It uses expression profiles and 
retention times of the putative ions to cluster them. Each cluster is then used to generate 
one spectrum containing the clustered ions (peaks). 

.. image:: msclust_summary.png 


-----

**Output**

values = stricter separation at the value determined in 'Potential Density reduction' above  
(TODO review this comment). 

*Stop Criterion:* When to stop reducing and looking for new clusters. Lower values = more iterations 

.. __: javascript:window.open('confidence_and_slope_params_explain.png','popUpWindow','height=700,width=800,left=10,top=10,resizable=yes,scrollbars=yes,toolbar=yes,menubar=no,location=no,directories=no,status=yes')


-----

**Output files described below**

*SPECTRA:* this file can be submitted to NIST for identification of the spectra.

`Click here for more details on the Sample selection and Spectrum peak intensity correction algorithm parameters related to SPECTRA generation`_  

.. _Click here for more details on the Sample selection and Spectrum peak intensity correction algorithm parameters related to SPECTRA generation: javascript:window.open('sample_sel_and_peak_height_correction.png','popUpWindow','height=700,width=800,left=10,top=10,resizable=yes,scrollbars=yes,toolbar=yes,menubar=no,location=no,directories=no,status=yes')

-----

*MIC:* stands for Measured Ions Count -> it contains, for each cluster, the sum of the ion count 
values (corrected by their membership) for all MEASURED cluster ions in the given sample.

by the membership value of the peak in the cluster in case the SIM peak is "shared". If the SIM peak is not 
"shared" then the "raw" intensity values of the SIM peak are recorded in the SIM file. 

`Click here for more details on the SIM output file`_  

.. _Click here for more details on the SIM output file: javascript:window.open('sample_SIM.png','popUpWindow','height=700,width=800,left=10,top=10,resizable=yes,scrollbars=yes,toolbar=yes,menubar=no,location=no,directories=no,status=yes')



  </help>
</tool>