Abstract: The present invention provides a method and an improved apparatus for removing gas bubbles from a reaction chamber comprising a flexible layer removably affixed to a substrate layer having a multiplicity of oligonucleotide binding sites disposed thereon, in which biological reactions are performed. The invention specifically relates to methods and apparatus for removing gas bubbles from a reaction chamber wherein target molecules contained in a sample fluid are reacted with probe molecules immobilized on a substrate having an array of oligonucleotide binding sites. The arrays are covered with a flexible, gas permeable layer that permits mixing of the sample fluid on the biochip and removal of gas bubbles from the fluid by use of a means for facilitating diffusion of gas bubbles across the flexible, gas permeable layer.