From the very beginning ...

Make sure you know this
Transfer your data to mchips e.g. via WinSCP (from remote, not needed from in-house)
Upload your data to M-CHiPS
- For ICP-data:
  ICP data are uploaded as one file per experiment (e.g. whole site) after picking appropriate wavelengths in Excel. For the file format please talk to Ricardo. Beware, this is the only M-CHiPS pipeline reading kommas instead of floating points.
- For Mass Spectrometry-data:
  Mass spectrometry data are acquired as raw files. Much like microarry images, they need to be processed with specialized software before import. As yet, following pipelines are implemented:
  - TMT6x (via Mascot Distiller)
  - label free (Progenesis/Mascot)
  - SILAC2x or 3x (MaxQuant/Andromeda)
- For Genepix-output:
  Before loading up your data, you have to divide your gpr-file into a file with the "green"-data and a file with the "red"-data. In addition, if you haven't analyzed (GenePix) the whole slide in one but in two or more smaller partitions, you have to combine your partitions. This is all done by the program "mergeblocks" (see also special cases)
  Connect to the server. When the text window appears, instead of typing mchips, type
  mergeblocks <enter> - this program will tell you step by step what to do
  Now your data are ready for loading up into your database. In the same directory type
  mchips <enter>
  Hit Data Import, Upload Experiment - and answer the questions until the upload starts.
- For Illumina or Affymetrix-data:
  Before transfering your data to the server, open your .xml file containing one signal per Gene with Excel, delete all columns but the first one (Affy-IDs) and the "Signal" - column. Save the file (with only 2 colunns remaining) as tab delimited text.
  Transfer the text files (one for each hybridization) to the server via WinSCP-session.
  Connect to the server (evt. cd to the folder where your data are) and start mchips. Hit Data Import, Upload Experiment - and answer the questions until the upload starts.
- All other imaging software:
  Connect to the server (evt. cd to the folder where your data are) and start mchips. Hit Data Import, Upload Experiment - and answer the questions until the upload starts.
Annotate your experiments
You have two alternatives for annotation:
- you can annotate your experiments first via www, and then load your data into this annotated experiment or
- you can load your data into a new, not yet annotated experiment, and annotate the experiment later.
Please find more information here.
Delete data
An experiment can be deleted by first deleting the comprised signal intensities, then deleting the annotations:
1. Connect to the server and start mchips. Hit Data Import, Delete Experiment - and answer the questions until the experiment is being deleted.
2. Delete annotatations e.g via www (with button "delete dropped experiment" atop the "quit" button).
Open M-CHIPS
Whenever working with M-CHIPS, be sure to be in the directory where your data are! M-CHIPS will also save results or default working parameters in this directory. So first go to the right directory, then type mchips <enter> and hit Analysis. Here you can either load a workspace file you saved the other day (i.e. from a previous analysis session) or load data from the database.