## page was renamed from CancerStemCellProject/VeroniqueVoisin/PathwayAnalysisService/SOP
#acl All:read

= Service Standard Operating Procedure (SOP) =
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==  Consulting Meeting ==
  * ~+'''Goal'''+~: to help plan an experiment before it is run. We can recommend case studies that user can learn from. 
     * Genomics technologies are very sensitive: they can detect small amounts of variation. A good experimental design considers all possible variables (or factors) and ensures better quality data. You are encouraged to come to talk with us about your planned experiment. Will the experimental design enable you to test your hypothesis and answer your questions?  Are there variables you did not think of? Do you have enough replicates? Do you use an appropriate control for your experiment? 
     * These consulting meetings can also generate a follow-up plan, where additional meetings can be scheduled during and after an experiment is run to answer questions: it is up to you to decide if you need the analysis or not. We are always available to discuss your data.
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== Analysis Planning Meeting ==
 * ~+'''Goal'''+~: To learn about your project and discuss pathway and network analysis options and their requirements.
 * Once correctly formatted input data are received and the quality is checked against analysis requirements, we will issue an '''initial pathway analysis plan''' (see below).
 * ~+'''Time estimate'''+~: 60 minutes   
 * ~+'''Initial Meeting and Data Input Requirement'''+~: please have these data and information ready:
    * '''During the initial meeting, we will discuss:'''
      * the biological question(s) you want to answer
      * the experimental design
      * the platform you used to generate your data (e.g Affymetrix or Illumina, the chip model,...)
      * analysis already completed
      * the quality controls and the required input data format

    * '''Your data should have been statistically analyzed and you need to provide us with 1 file (.txt) for pathway and network analysis''':
    [[CSCPathwayAnalysisService/Data| MORE DETAILS FOLLOWING THIS LINK ]] or look at the [[CSCBiostatService | BIOSTATISTICS SERVICE ]].
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==  Analysis ==

 * ~+ '''Pathway Analysis Plan''' +~  
  * ~+Goal:+~  A pathway analysis plan is a document that states the different analyses that will be performed and a completion time estimate. We write the pathway analysis plan once correctly formatted input data are received. It needs to be signed off by researchers leading the project and the lead P.I.
  * A meeting can be scheduled if requested to explain the Pathway Analysis Plan.

 * ~+ '''Run analysis, interpret the results and produce a report'''+~
  * ~+'''Status :'''+~ the analysis status is visible on the website page (see at the end of the page); We will communicate with you very regularly during the process to ensure effective interpretation of results. 
  * ~+'''Analysis Report'''+~: A report will include an overview of the results and a detailed focus analysis of interesting pathways will be written at the end of the analysis.
  * ~+ '''Result Meeting'''+~
   * Goal: discuss the analysis and report. 
       * Examples of questions we can discuss: Do the results meet your expectations?
                                Is there anything unexpected in the results?
                                If you had the resources, which experiments would you conduct based on the results of this analysis?
   * Time estimate: 30 to 60 minutes
   * Two options are available after this meeting: 
     * We need to perform additional bioinformatics analyses: custom analyses 
     * You are satisfied with the results and you explore the data and results using available software tools that we provide and then perform some validation experiments before an optional follow-up meeting
             

 * ~+ ''' Training session ''' +~ 
  * ~+Goal:+~ You can schedule a training session if you wish to do your own pathway and network analysis or explore results we have generated. We will explain how to install the required software and how to use it to explore your data. 
  * ~+Time estimate+~: 30 to 60 minutes
  * [[CSCPathwayAnalysisService/Tutorials | Link to Tutorial Page ]]
 * ~+ '''Custom analyses''' +~ 
  *  Meeting with Researcher to explain the results of the custom analyses

 * ~+ '''Follow-up''' +~  
  * Goal: you may have performed validation experiments or generated new research hypotheses based on your genomics study. You may need to go back and focus on a different aspect of your data. We can help you to re-analyse your data, provide additional bioinformatics tools or help plan a subsequent genomics experiment.

 * ~+ '''Analysis Flowchart:''' +~ 
{{attachment:flowchart2b.png}}
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 *[[CSCPathwayAnalysisService | BACK TO HOME PAGE ]]