M-CHIPS home

Manual
Getting Started
Starting M-chips
Loading data
Normalizing the data
Filtering the data
Exploring the data

FAQs

UNIX

Questions, comments, contributions?

Loading data: the M-CHIPS browser

  • Browsing:
    • Choose one MCE (multi conditional experiment) by clicking once on it.
    • The conditions of this MCE will appear in a separate column on the right - mark one condition by clicking once on it.
    • The numbers of the uploaded hybridizations in this condition will appear in a separate column on the right (each number relates to a certain data-file, once you have uploaded it, it will never change although previous uploaded data-files might be discarded - this is important to ensure that you are working with the right data).
    • If you click on the black-arrow button (on the right side under the columns), condition- and measurement-dependent experiment annotations will be shown.
    • If you click on the similar arrow-button again (now pointing in the other direction) experiment annotations are hidden again.
    • If you click on the const.-button a Netscape window will open (if not, you have to open one by yourself), displaying the constant experiment annotations of the marked MCE.

  • Selection:

    • Select-button
      • Click on the red select-button: some more red arrows and other buttons and 3 more columns will appear at the bottom.
      • You are able to select uploaded MCEs or to recombine conditions or hybridizations to a new dataset for analysis.
      • Anything you want to analyze is chosen with the help of the red arrows in the middle of the window.
    • Button with 3 arrows pointing down
      takes the whole dataset (all MCEs you have defined) into the selection.
    • Buttons with 1 arrow pointing down
      select the marked item (MCE, condition or hybridization) from the column above for analysis.
    • Buttons with 1 arrow pointing right down
      • select the marked item (MCE or condition) from the column above for analysis but puts them in the next (more right) category-column.
      • With this you are e.g. able to define a whole MCE as a condition of a new designed MCE you now want to analyze (at this step you don't have to care about defined experiment annotations, because mchips will recognize the changed "environment" and re-arrange e.g. the condition-dependent annotations itself).
    • Most left del-button
      deletes the whole selection.
    • Del-buttons next to selection column
      delete marked items from selection.
    • Start of analysis
      • If you have selected your appropriate dataset, you can start analysis by clicking the "Edit" and select the required "Filter" for filtering the data. Click the blue "Analysis" field to do further analysis. (if you have chosen only 2 hybs., you have the possibility to generate a scatter plot).
      • When you are working with radioactive arrays, you are asked if you want to work in a monochannel mode: press "ok".
      • Now the process starts and after a while you have the possibility to save your dataset (you can just go on by pressing "return").