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The whole process includes the selection and treatment of the glass substrates, visual monitoring and recording the deposition of each element printed on the array, and the final characterization and hybridization of statistically representative samples of arrays from each lot produced We do quality control our arrays at every step of the process. The arrays that the customer receive are the ones that passed these quality control. The combination of microarray printing know-how, technology innovation, in process QC and industrialization forms the basic for Agilent Sure Print technology.
This is an example of a QC microarray which is manufactured with every customer run.  The QC microarrays have 100s and 1000s of replicate probes to determine the performance of the SurePrint ink-jet manufacturing process.
Use for writing papers
So the first question to be asked is what types of data are we trying to represent. And what is the minimal information that can be given about a microarray experiment to allow it to be reproduced and compared to other experiments. This is the focus for the first standard: the minimum information about a microarray experiment (MIAME).
First we will describe the raw data being processed. The raw data is generally provide as image data, scanned from microarray chips produced from different hybridizations. Some of these images may be from diseased samples, and some from control (or normal) samples. The spots in these images are then quantified, using image analysis software, and the results from this are put into a quantification matrix (with one matrix for each image). The index along one dimension of this matrix gives the actual spot being quantified on the image, the other dimension gives different quantification measures such as overall integrated intensity, spot size, medium intensity, etc. The quantification matrices are then used to produce a single gene expression data matrix. The gene expression matrix gives the overall expression value for each gene, in each sample. The next slide will give more details about the gene expression matrix.
There are a number of reasons why this is a two stage process. There is not always a one-to-one relationship between the quantification values in the quantification matrices, and the gene expression values in the gene expression matrix, for example:
1.The DNA may have been spotted in a number of locations on the array (physical replicates). The quantification matrix gives different values for each of these spots whereas they nee to be combined into a single expression value in the gene expression matrix.
2.There may be a number of arrays hybridized to the same sample (again physical replicates),  the quantifications from the same spots on these different arrays also need to combined into a single expression value.
3.Different ‘regions' of DNA from the SAME gene may be spotted at different locations on an array. These different measurements also need to be combined into a single value for the expression level of this gene.