Described herein are in situ synthesized arrays and methods of making them, wherein array signal sensitivity and robustness is enhanced by carrying out conditioning steps and/or generating linkers during synthesis. An array comprises a surface with a collection of features, wherein the features comprise molecules or polymers attached to the surface. In certain embodiments of the invention, carrying out conditioning steps during array synthesis can yield arrays with improved signal. In other embodiments, linkers are synthesized on the array surface prior to synthesis of functional molecules, wherein increasing linker length can correspond to an improvement in the signal generated by the array.