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?

• Accounts
  Please talk to Kurt in order to get an account.

• Experiment annotation definitions
  Meanwhile there will be time to think about how to annotate your experiments. Both sample biology and experiment should be covered at a considerable level of detail. Please provide a list of annotation definitions like these. If in doubt about taking into account more or less parameters, please consider this. You may want to recombine different lists or simply use the one closest to your demands as a basis for designing your own. Please import the tab delimited list(s) into any spreadsheet program. The list format is explained here. You may ignore the numbering of both annotations and values and omit the numbers for added lines. Only the lastheadingno is essential for linking the annotations to their particular headings.

• Data example
  For Mass Spectrometry data, please refer to TMT6x, label free (Progenesis), SILAC (MaxQuant)

  In the following, I assume that you are using either Affymetrix or Illumina platforms or the Genepix imaging program. If not, please let me know. We already parsed from Bioimage, AIS and Xdigitize output (as well as from Decider importing 2D-DIGE gels). Otherwise,I will need to hack something tailor-made.

  • For Illumina or Affymetrix data, please prepare an example file like this: 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.

  • For genepix, you will need to generate your own . gal file using array-list generator and perhaps spotconverter and fpln.pl (in case you spot both duplicates within the same block). Please provide a genepix output file, ID column containing field (just enter `1' for all IDs unless you expect to have differentially behaving partitions), plate, letter and number (i.e. microtiter plate location) - separated by underscores. Code the letter as number (A becomes 1, B becomes 2, ...) and let all numbers have 2 digits. Example: "01_07_16_13". The file may look like this.
    M-CHiPS requires duplicate spotting! To check if every ID occurs exactly twice, please use

    testgplist

    on any TBI machine. You can locate IDs promted to occur more or less than 2x e.g. in word, excel or staroffice (edit-search). If you have problems negotiating with genepix, ask Verena or Frank or Susanne or Andrea or anyone who did it (i.e. not me).
    Please also let me know for every ID, which of the following classes it belongs to:

    g - genes
    h - heterologous DNA of unknown conc. (e.g. guidespots)
    k - heterologous DNA of which the concentration of the target is known (any spot intended for spiking)
    e - empty spots (please also provide the degree of emptyness, e.g. untreated surface or spotting buffer
    r - reference spots (any spot not fitting in above categories)

    You can do that in a simple way, such as 'names belonging to k begin with "laber", "rhabarber" or "blabla", e always named "empty", rest g' or so in an email. In this case please also tell me the number of comprised spot-duplicates for every category (so that I can check the according data base tables). That's it.

    By the way .. latest genepix research revealed a considerable timesaving potential of testing the first genepix output file before producing many more :-). Ok, because that last sentence was not understood by all of us: Give us the first .gpr file you create and STOP PRODUCING MORE until this first one is in the database!!! We will not help anyone anymore who ignores this.

• GenePix best practice
  
  • Use Genepix 4.1 and save normally.
  • Do not flag misbehaving spots (will make things worse).
  • Additionally save the (manually adapted) grid for any .gpr file.
  • Stop producing .gpr files until the first one is checked.

• Mailing list
  If you want to join discussions about new common annotations or to be alerted when new features have been implemented, you can join our email list.

• Access
  Annotator and Results can be accessed via web interface. The analysis suite can be accessed via ssh or better Nx connection from any Unix-, Linux-, or Windows-Computer.