Combining case and control sample from 2 different datasets

Question

[babak1146]

Can I Combine case and control microarray samples from 2 different datasets? Note: Two samples are same platform and same tissue (agilent 2-color platform: GPL6480)

[WouterDeCoster]

Please elaborate on the number of samples and how the groups are split across technologies, ideally in a table format. Don't make us guess your experimental setup. Also add what you aim to do with your data, which the endpoint is of your analysis and chose sensible tags for your thread.

[babak1146]

i have 2 datasets.

1-GSE53845 (Disease : IPF) 
    Platform: GPL6480 (Agilent-014850 Whole Human Genome Microarray 4x44K G4112F )
2-GSE69497 (Disease: Asthma)  
   Platform: GPL6480 (Agilent-014850 Whole Human Genome Microarray 4x44K G4112F )

i want to use IPF control samples for Asthma. for DEGs and feature selection i need them. can i do it?