8.5 years ago by
Maastricht, The Netherlands
Well the XKCD answer mentioned by Keith is good to have in mind, but of course not a reason to give up all efforts to create standards or to try to improve data and software interoperability.
Keith is right though that microarray data do not easily give absolute expression values and it is almost impossible to compare absolute expression values across experiments and across technologies. Microarray data are indeed more suited for comparisons between conditions than for absolute expression values.
But then you can of course ask zjk's question again. Can't you easily create a standardized format or at least a standardized content for microarray expression data comparison? Of course in that case you would need to specify what conditions (and thus what groups of arrays) you would want to compare. And that asks for another type of standardization: the experiment description files. In fact there are interesting efforts for that like the now almost traditional MageTab format or the new Isa-tab that also covers other types of omics.
The standardized result should be based on standardized data treatment for QC, normalization and such and should then give you a p-value for the statistics (an ANOVA if you have more than one comparison is a good start) and the various fold changes for the comparisons. This plus the probeset identifiers (which can easily be resolved to genes, but which keeps the raw information), was precisely what we stored as a network wide standard in [?]NuGO[?]. The same type of information is also provided by [?]Gene Expression Atlas[?]. Since that is a repository of selected (from Arrayexpress) good quality expression studies with data treatment and result storage in a standardized way, I would suggest to use the Gene Expression Atlas data format as the de facto standard for microarray comparison data, unless you have a really good reason to do otherwise. In fact that is what we plan to do in the [?]dbNP[?] project.
modified 8.5 years ago
8.5 years ago by
Chris Evelo ♦ 10.0k