If I understand you correctly you try to use lots of data from GEO and your software thinks that some of it is not good enough. You should be careful about cheating your software in thinking differently since it might actually be right. Not all data in repositories is as good as it should be.

If you are not looking for specific sets that really need to be fixed I would suggest an alternative approach. For the European counterpart of GEO, ArrayExpress: (https://www.ebi.ac.uk/arrayexpress/ ), there is a curated and quality controlled and in part standard treated subset available at Expression Atlas (https://www.ebi.ac.uk/gxa/home). This might serve your purposes better.