Questions, comments, contributions?
In order to use M-CHiPS, you will have to have an account for certain DKFZ
machines. Please also provide experiment annotation definitions as well as a
sample imaging output in a certain format. You will then get your own
organism- or field-specific M-CHiPS database.
(How to obtain a database)
At your service,
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
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
- 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
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
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
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
- 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
Results can be accessed via web
interface. The analysis suite can be accessed via ssh or better Nx connection from any Unix-, Linux-, or