Results section

Data are stored in M-CHIPS as multiconditional experiments (MCEs). A result
may either represent a single MCE or is a recombination of conditions and/or
measurements stemming from different multiconditional experiments.
Experiment annotations can be viewed both in the original form, i.e. for the
experiments and recombined for the results. For each result, the comprised
data have been at least normalized and filtered. Visually supervised
normalization as well as choice of filter parameters have been done by the
analyst stated in the comment. There may be different types of results:

Comprehensive list

The complete data set as tab-delimited ASCII file. The tables include raw
and fitted (i.e. normalised) intensities for each individual measurement as
well as ratios which were calculated by division of each individual
hybridization by the gene wise median of all control hybridizations for
monochannel (radioactive) data and by division of each channel by the
corresponding control channel of the same hybridization for multichannel
data. In addition the medians and reproducibility measures [1] for repetitive
measurements are provided.

Color-coded list

These lists comprise factors of relative changes with respect to the control
condition and the median value of normalised signal intensities.
Significance levels were assessed by two reproducibility criteria as described [1].
The highly stringent `min-max separation' is
calculated by taking the minimum distance between all data points of one
condition and all data points of the control condition. The less stringent
criteria, called `standard deviation separation', is defined as the
difference of the means of the two data sets diminished by one standard
deviation. In the tables, a colour-code indicates the two stringency
measures. According to these criteria, data were classified as being of
high or medium significance:

In case the last line of the header specifies the color-code as p-value based,
(high) significance corresponds to p<0.05 (0.01) as computed by limma eBayes.

Upregulations are marked by warm (red and yellow), downregulations by cold
colors (blue and light blue); high reproducibility is shown by dark (red and
blue), medium reproducibility by light colors (yellow and light blue). If none
of the two criteria is fulfilled the signal should by regarded as not reliable
- even if a high ratio is displayed - and is tagged white in the color coded list.

in preparation: Reports containing text and figures

We are implementing means to easily attach results such as correspondence
analysis plots [2] and other figures to the data. They will come along with a
textual description of marked clusters or associations.


Beißbarth, T., Fellenberg, K., Brors, B., Arribas-Prat, R., Boer, J. M., Hauser, N. C., Scheideler, M., Hoheisel, J. D., Schütz, G., Poustka, A., & Vingron, M. (2000)
Bioinformatics, 16, 1014-1022. [abstract] [pdf]

Fellenberg, K., Hauser, N. C., Brors, B., Neutzner, A., Hoheisel, J. D., and Vingron, M. (2001)
Proc. Natl. Acad. Sci. U.S.A., 98, 10781-10786. [abstract] [pdf]