Maybe you can try with some library to manipulate .CEL files and change gene names or expression levels. Presumably, this will require that you change the array description file too (e.g., ADF), and even with that I'm not sure that this way you'll pass data quality checking that is run by GEO managers. The same for ArrayExpress (I am one of the developers of the latter).

Moreover, in my opinion that is not the way GEO or ArrayExpress should be used. These repositories are intended to make data public, to share them among the scientific community and to allow your colleagues to verify your data analysis. And if your work is paid by public funds, I think your intent is not quite fair.

If it's an editor that is originating your problem (i.e., they don't accept your article, unless you store data in a repository), maybe you're allowed to use a small repository of yours (e.g. using BASE, ISA-Tools or Gene Expression Atlas) and make the data available on request or licence-based. Though that's not an easy task if you don't have an IT administrator. Not sure they accept a simple form of publication, consisting in formatting your experiment description according to a format like MAGE-TAB and putting this + .CEL files in a web server, that you can password-protect.

Last thing, ArrayExpress gives you the option to keep your data private for up to 1 year, but eventually they have to become public.

I think Marco Brandizi is correct in suggesting not to manipulate files to be published on GEO or ArrayExpress. GEO also gives you one year before disclosure.

The idea of making data publicly available is for other researcher to either use or verify your data. Any changes you make in your original .CEL file could be considered (in fact ARE) falsification of data, so you don't want to do that.

GEO allows you to hold back the publication of your uploaded data, giving you more than enough time to work on your favorite genes before someone else picks it up. Alternatively, publish your manuscript in a journal that does not require you to make your .CEL files public.

As mentioned by others, falsifying your data is not the way forward. I do agree though, that in a competative research field you do not necessarily want to release your ideas and genes to the wider community, where big groups will turn around your findings in record time and beat you to the publication. It is a continual balance between contributing to the wider research community, but also maintaining a viable and fundable research strategy locally. The other option is to submit only a proportion of your expression data, that demonstrates your submitted findings but minimizes any risk of losing the edge on your current and future work.

Hi guys, thank you all very much for the suggestions, especially Marco. I will discuss with our system manager for a repository and of course will communicate with GEO to see the best options.

Are you going to publish this data in a paper? If not...WHy are you submitting to GEO in the first place? WHat you are prosposing is not only unethical it is likely against he guide lines of your university. This would be concidered acedemic misconduct you could be expelled, and if your supervisor is putting you up to this they could be fired. If the only edge you can keep over your competition is the name of a gene or a new technique you will eventually be beat. Your competitive edge must come from your understanding and insight into your feild of study. Your ideas and experimental approach must be novel. Lastly, your work, your University even your salary are all likely funded if not fully, largely from tax money. You do not own your work. the Tax payer does. There is no private information. If you think you have somethinhg really important, file a patent, otherwise share your knowledge, its how you got to be where you are. Think of the other research you read and dependend on to get to where you are. WHat if all of those people decided to hold back key peices of information? How would science progress?