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data/controlled_vocab/ALS_SpotTypeWannabe.xml.new  view on Meta::CPAN

</comment>
<term name="cdna"
        description="the complete cloned  cds of a protein"/>
<term name="partial_cdna"
        description="the piece of a cloned EST described by start and stop positions"/>
<term name="synthetic_oligo"
        description="a synthetic DNA oligomer, sequence as described"/>
<term name="pcr_product"
        description="the amplified section of a an EST, full-length cDNA or other sequence feature"/>
<term name="gdna_sequence"
        description="the sequence of a fragment derived from a genomic source"/>
<term name="control_intensity_range"
        description="allows the dynamic range of signal detection to be estimated"/>
<term name="control_nonspecific_binding"
        description="Allows the noise from non-specific binding to be estimated"/>
<term name="control_target_concentration"
        description="Allows the effect of target concentration on signal intensity to be estimated"/>
<term name="control_kinetic"
        description="For the purpose of assessing the effect of hybridization conditions and target complexity on the kineticsof reannealing"/>
<term name="control_dilution_series"
        description="serial dilution for signal response curve"/>

data/controlled_vocab/AL_Medium.xml  view on Meta::CPAN

        description="user sequence features are spotted on a rigid silicon-based support medium"/>
<term name="nylon_membrane"
        description="user sequence features are spotted on a nylon-coated flexible medium"/>
<term name="nitrocellulose"
        description="user sequence features are spotted on a nitrocellulose medium"/>
<term name="gel_sieve"
        description="target sequence features are separated through a size sieving procedure"/>
<term name="mag_bead"
        description="target sequence features are separated by magnetic bead attachment"/>
<term name="sequence_instance"
        description="target sequence features are  sequenced fragments whose frequency of occurrence is recorded"/>
</controlled_vocabulary>

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data/db_tables/protocols.xml  view on Meta::CPAN

 produced when things work well. The contrast in this image has been adjusted to allow faint spots to
 be easily visualized. Important aspects of the hybridization to note are the low level, uniform
 background and the good signal-to-noise

 Image Processing

 Image processing involves three stages. First, the spots representing the arrayed genes must be
 identified and distinguished from spurious signals that can arise due to precipitated probe or other
 hybridization artifacts or contaminants such as dust on the surface of the slide. This task is simplified
 to a certain extent because the robotic arraying systems used to construct the arrays produce a regular
 arrangement of the spotted DNA fragments. However, variable intensities and uneven slide
 backgrounds as well as some irregularities in the gridded arrays complicate the problem slightly.
 Generally, problem of grid spot location is coupled with estimation of the fluorescence background.
 For microarrays, it is important the background be calculated locally for each spot, rather than globally
 for the entire image as uneven background can often arise during the hybridization process. The second
 step in analysis of the array images is the estimation of background.
 Following spot identification and local background determination, the background-subtracted
 hybridization intensities for each spot must be calculated. There are currently two schools of thought
 regarding the calculation of intensities - the use of the median or the mean intensity for each spot. As
 array analysis generally uses ratios of measured Cy3 to Cy5 intensities to identify differentially
 expressed genes, the mean and the integrated intensities are operationally equivalent. In comparisons