Changeset 1938


Ignore:
Timestamp:
Feb 8, 2006, 9:26:33 AM (17 years ago)
Author:
Nicklas Nordborg
Message:

Added QuantArray? raw data types
Added some intensity formulas to other raw data types
Added MAGE files describing raw data types

Location:
trunk
Files:
14 added
1 edited

Legend:

Unmodified
Added
Removed

  • trunk/src/raw-data-types.xml

    r1937 r1938  
    447447      type="float"
    448448    />
     449    <intensity-formula
     450      name="QImageConst"
     451      title="Q(image,const)"
     452      description="Spot intensity based on user-provided diameter and measured data"
     453      >
     454      <formula
     455        channel="1"
     456        expression="raw('QImageConst')"
     457      />
     458    </intensity-formula>
     459    <intensity-formula
     460      name="QImageVar"
     461      title="Q(image,var)"
     462      description="Spot intensity based on computed diameter and measured data"
     463      >
     464      <formula
     465        channel="1"
     466        expression="raw('QImageVar')"
     467      />
     468    </intensity-formula>
     469    <intensity-formula
     470      name="QFitConst"
     471      title="Q(fit,const)"
     472      description="Spot intensity based on user-provided diameter and theoretical fit to the data"
     473      >
     474      <formula
     475        channel="1"
     476        expression="raw('QFitConst')"
     477      />
     478    </intensity-formula>
     479    <intensity-formula
     480      name="QFitVar"
     481      title="Q(fit,var)"
     482      description="Spot intensity based on computed diameter and and theoretical fit to the data"
     483      >
     484      <formula
     485        channel="1"
     486        expression="raw('QFitVar')"
     487      />
     488    </intensity-formula>
    449489  </raw-data-type>
    450490 
    … …  
    17321772      type="float"
    17331773    />
     1774    <intensity-formula
     1775      name="medianfg"
     1776      title="Median FG"
     1777      description="Median foreground"
     1778      >
     1779      <formula
     1780        channel="1"
     1781        expression="raw('medCy3')"
     1782      />
     1783      <formula
     1784        channel="2"
     1785        expression="raw('medCy5')"
     1786      />
     1787    </intensity-formula>
     1788    <intensity-formula
     1789      name="median"
     1790      title="Median FG - Median BG"
     1791      description="Subtract median background from median foreground"
     1792      >
     1793      <formula
     1794        channel="1"
     1795        expression="raw('medCy3') - raw('bgCy3')"
     1796      />
     1797      <formula
     1798        channel="2"
     1799        expression="raw('medCy5') - raw('bgCy5')"
     1800      />
     1801    </intensity-formula>
    17341802  </raw-data-type>
    17351803 
    … …  
    17421810    >
    17431811  </raw-data-type>
     1812  -->
    17441813 
    17451814  <raw-data-type
    17461815    id="quantarraybiotin"
    1747     channels="2"
     1816    channels="1"
    17481817    name="QuantArray Biotin"
    17491818    table="RawDataQuantArrayBiotin"
    17501819    >
     1820    <property
     1821      name="Number"
     1822      title="Number"
     1823      description="Number."
     1824      column="number"
     1825      type="int"
     1826    />
     1827    <property
     1828      name="BiotinIntensity"
     1829      title="Intensity"
     1830      description="Mean pixel biotin foreground intensity in biotin channel."
     1831      column="intensity"
     1832      channel="1"
     1833      type="float"
     1834    />
     1835    <property
     1836      name="BiotinBackground"
     1837      title="Background"
     1838      description="Mean pixel biotin background intensity in biotin channel."
     1839      column="background"
     1840      channel="1"
     1841      type="float"
     1842    />
     1843    <property
     1844      name="BiotinDiameter"
     1845      title="Diameter"
     1846      description="Average diameter of the spot (in microns). Used to determine whether the spot is close to the expected size or is perhaps an artifact on the slide."
     1847      column="diameter"
     1848      channel="1"
     1849      type="float"
     1850    />
     1851    <property
     1852      name="BiotinArea"
     1853      title="Area"
     1854      description="The area of the spot given as the number of pixels (in sq. microns). Used to determine whether the spot is close to the expected size or is an artifact on the slide."
     1855      column="area"
     1856      channel="1"
     1857      type="int"
     1858    />
     1859    <property
     1860      name="BiotinFootprint"
     1861      title="Footprint"
     1862      description="The distance between the expected position of a spot and its actual measured position (in microns)."
     1863      column="footprint"
     1864      channel="1"
     1865      type="float"
     1866    />
     1867    <property
     1868      name="BiotinCircularity"
     1869      title="Circularity"
     1870      description="Reports the degree to which a spot is close to a perfect circle. This measurement is used to determine the print quality of the microarray."
     1871      column="cirularity"
     1872      channel="1"
     1873      type="float"
     1874    />
     1875    <property
     1876      name="BiotinSpotUniformity"
     1877      title="Spot uniformity"
     1878      description="The uniformity of the pixels used in the spot foreground intensity calculation. This helps in determining the quality of the spot and aids in selecting the correct quantification output method."
     1879      column="uniformity"
     1880      channel="1"
     1881      type="float"
     1882    />
     1883    <property
     1884      name="BiotinBkgUniformity"
     1885      title="Background uniformity"
     1886      description="The uniformity of the pixels used in the background intensity calculation."
     1887      column="bg_uniformity"
     1888      channel="1"
     1889      type="float"
     1890    />
     1891    <property
     1892      name="BiotinSignalNoiseRatio"
     1893      title="Signal noise ratio"
     1894      description="The ratio of spot intensity to the standard deviation of the local background of all spots in the microarray. Spots with a low Signal/Noise Ratio can be quickly identified for later reviews."
     1895      column="snr"
     1896      channel="1"
     1897      type="float"
     1898    />
     1899    <property
     1900      name="BiotinConfidence"
     1901      title="Confidence"
     1902      description="Confidence."
     1903      column="confidence"
     1904      channel="1"
     1905      type="int"
     1906    />
     1907    <property
     1908      name="IgnoreFilter"
     1909      title="Ignore filter"
     1910      description="Whether the feature quantitation is used in down-stream analysis (flagging feature as valid): 0 = feature invalid (null data); 1 = feature valid."
     1911      column="ignore_filter"
     1912      type="int"
     1913    />
     1914    <property
     1915      name="BiotinRatio"
     1916      title="Ratio"
     1917      description="The portion of the overall spot fluorescence contributed by biotin channel (normalized so that biotin channel contribution equals 1)."
     1918      column="ratio"
     1919      channel="1"
     1920      type="int"
     1921    />
     1922    <property
     1923      name="BiotinPercent"
     1924      title="Percent"
     1925      description="The portion of the overall spot fluorescence contributed by biotin channel (in percent)."
     1926      column="precent"
     1927      channel="1"
     1928      type="float"
     1929    />
     1930    <property
     1931      name="BiotinDiameterFilter"
     1932      title="Diameter filter"
     1933      description="Biotin diameter filter."
     1934      column="diameter_filter"
     1935      type="int"
     1936    />
     1937    <property
     1938      name="BiotinAreaFilter"
     1939      title="Area filter"
     1940      description="Biotin area filter."
     1941      column="area_filter"
     1942      type="int"
     1943    />
     1944    <property
     1945      name="BiotinFootprintFilter"
     1946      title="Footprint filter"
     1947      description="Biotin footprint filter."
     1948      column="footprint_filter"
     1949      type="int"
     1950    />
     1951    <property
     1952      name="BiotinCircularityFilter"
     1953      title="Circularity filter"
     1954      description="Biotin circularity filter."
     1955      column="circularity_filter"
     1956      type="int"
     1957    />
     1958    <property
     1959      name="BiotinSpotUniformityFilter"
     1960      title="Spot uniformity filter"
     1961      description="Biotin spot uniformity filter."
     1962      column="uniformity_filter"
     1963      type="int"
     1964    />
     1965    <property
     1966      name="BiotinBkgUniformityFilter"
     1967      title="Background uniformity filter"
     1968      description="Biotin background uniformity filter."
     1969      column="bg_uniformity_filter"
     1970      type="int"
     1971    />
     1972    <property
     1973      name="BiotinSignalNoiseRatioFilter"
     1974      title="Signal noise ratio filter"
     1975      description="Biotin signal noise ratio filter."
     1976      column="snr_filter"
     1977      type="int"
     1978    />
     1979    <property
     1980      name="BiotinReplicateFilter"
     1981      title="Replicate filter"
     1982      description="Biotin replicate filter."
     1983      column="replicate_filter"
     1984      type="int"
     1985    />
     1986    <intensity-formula
     1987      name="meanfg"
     1988      title="Mean FG"
     1989      description="Mean foreground intensity"
     1990      >
     1991      <formula
     1992        channel="1"
     1993        expression="raw('intensity')"
     1994      />
     1995    </intensity-formula>
     1996    <intensity-formula
     1997      name="mean"
     1998      title="Mean FG - Mean BG"
     1999      description="Subtract mean background from mean foreground"
     2000      >
     2001      <formula
     2002        channel="1"
     2003        expression="raw('BiotinIntensity') - raw('BiotinBackground')"
     2004      />
     2005    </intensity-formula>
    17512006  </raw-data-type>
    17522007 
    … …  
    17572012    table="RawDataQuantArrayCy"
    17582013    >
     2014    <property
     2015      name="Cy3Intensity"
     2016      title="Mean Cy3 intensity"
     2017      description="Mean pixel Cy3 foreground intensity in Channel Cy3."
     2018      column="cy3_mean"
     2019      channel="1"
     2020      type="float"
     2021    />
     2022    <property
     2023      name="Cy3Background"
     2024      title="Mean Cy3 background"
     2025      description="Mean pixel Cy3 background intensity in Channel Cy3."
     2026      column="cy3_mean_bg"
     2027      channel="1"
     2028      type="float"
     2029    />
     2030    <property
     2031      name="Cy3Diameter"
     2032      title="Cy3 spot diameter"
     2033      description="Average diameter of the spot (in microns). Used to determine whether the spot is close to the expected size or is perhaps an artifact on the slide."
     2034      column="cy3_diameter"
     2035      channel="1"
     2036      type="float"
     2037    />
     2038    <property
     2039      name="Cy3Area"
     2040      title="Cy3 spot area"
     2041      description="The area of the spot given as the number of pixels (in sq. microns). Used to determine whether the spot is close to the expected size or is an artifact on the slide."
     2042      column="cy3_area"
     2043      channel="1"
     2044      type="int"
     2045    />
     2046    <property
     2047      name="Cy3Footprint"
     2048      title="Cy3 footprint"
     2049      description="The distance between the expected position of a spot and its actual measured position (in microns)."
     2050      column="cy3_footprint"
     2051      channel="1"
     2052      type="float"
     2053    />
     2054    <property
     2055      name="Cy3Circularity"
     2056      title="Cy3 circularity"
     2057      description="Reports the degree to which a spot is close to a perfect circle. This measurement is used to determine the print quality of the microarray."
     2058      column="cy3_circularity"
     2059      channel="1"
     2060      type="float"
     2061    />
     2062    <property
     2063      name="Cy3SpotUniformity"
     2064      title="Cy3 spot uniformity"
     2065      description="The uniformity of the pixels used in the spot foreground intensity calculation.This helps in determining the quality of the spot and aids in selecting the correct quantification output method."
     2066      column="cy3_uniformity"
     2067      channel="1"
     2068      type="float"
     2069    />
     2070    <property
     2071      name="Cy3BkgUniformity"
     2072      title="Cy3 background uniformity"
     2073      description="The uniformity of the pixels used in the background intensity calculation."
     2074      column="cy3_bg_uniformity"
     2075      channel="1"
     2076      type="float"
     2077    />
     2078    <property
     2079      name="Cy3SignalNoiseRatio"
     2080      title="Cy3 signal noise ratio"
     2081      description="The ratio of spot intensity to the standard deviation of the local background of all spots in the microarray. Spots with a low Signal/Noise Ratio can be quickly identified for later reviews."
     2082      column="cy3_snr"
     2083      channel="1"
     2084      type="float"
     2085    />
     2086    <property
     2087      name="Cy3Confidence"
     2088      title="Cy3 confidence"
     2089      description="Unused QuantArray feature, will always = 1."
     2090      column="cy3_confidence"
     2091      channel="2"
     2092      type="int"
     2093    />
     2094    <property
     2095      name="Cy5Intensity"
     2096      title="Mean Cy5 intensity"
     2097      description="Mean pixel Cy5 foreground intensity in Channel Cy5."
     2098      column="cy5_mean"
     2099      channel="2"
     2100      type="float"
     2101    />
     2102    <property
     2103      name="Cy5Background"
     2104      title="Mean Cy5 background"
     2105      description="Mean pixel Cy5 background intensity in Channel Cy5."
     2106      column="cy5_mean_bg"
     2107      channel="2"
     2108      type="float"
     2109    />
     2110    <property
     2111      name="Cy5Diameter"
     2112      title="Cy5 spot diameter"
     2113      description="Average diameter of the spot (in microns). Used to determine whether the spot is close to the expected size or is perhaps an artifact on the slide."
     2114      column="cy5_diameter"
     2115      channel="2"
     2116      type="float"
     2117    />
     2118    <property
     2119      name="Cy5Area"
     2120      title="Cy5 spot area"
     2121      description="The area of the spot given as the number of pixels (in sq. microns). Used to determine whether the spot is close to the expected size or is an artifact on the slide."
     2122      column="cy5_area"
     2123      channel="2"
     2124      type="int"
     2125    />
     2126    <property
     2127      name="Cy5Footprint"
     2128      title="Cy5 footprint"
     2129      description="The distance between the expected position of a spot and its actual measured position (in microns)."
     2130      column="cy5_footprint"
     2131      channel="2"
     2132      type="float"
     2133    />
     2134    <property
     2135      name="Cy5Circularity"
     2136      title="Cy5 circularity"
     2137      description="Reports the degree to which a spot is close to a perfect circle. This measurement is used to determine the print quality of the microarray."
     2138      column="cy5_circularity"
     2139      channel="2"
     2140      type="float"
     2141    />
     2142    <property
     2143      name="Cy5SpotUniformity"
     2144      title="Cy5 spot uniformity"
     2145      description="The uniformity of the pixels used in the spot foreground intensity calculation.This helps in determining the quality of the spot and aids in selecting the correct quantification output method."
     2146      column="cy5_uniformity"
     2147      channel="2"
     2148      type="float"
     2149    />
     2150    <property
     2151      name="Cy5BkgUniformity"
     2152      title="Cy5 background uniformity"
     2153      description="The uniformity of the pixels used in the background intensity calculation."
     2154      column="cy5_bg_uniformity"
     2155      channel="2"
     2156      type="float"
     2157    />
     2158    <property
     2159      name="Cy5SignalNoiseRatio"
     2160      title="Cy5 signal noise ratio"
     2161      description="The ratio of spot intensity to the standard deviation of the local background of all spots in the microarray. Spots with a low Signal/Noise Ratio can be quickly identified for later reviews."
     2162      column="cy5_snr"
     2163      channel="2"
     2164      type="float"
     2165    />
     2166    <property
     2167      name="Cy5Confidence"
     2168      title="Cy5 confidence"
     2169      description="Unused QuantArray feature, will always = 1."
     2170      column="cy5_confidence"
     2171      channel="2"
     2172      type="int"
     2173    />
     2174    <property
     2175      name="IgnoreFilter"
     2176      title="Ignore filter"
     2177      description="Whether the feature quantitation is used in down-stream analysis (flagging feature as valid): 0 = feature invalid (null data); 1 = feature valid."
     2178      column="ignore_filter"
     2179      type="int"
     2180    />
     2181    <property
     2182      name="Cy3Ratio"
     2183      title="Cy3 ratio"
     2184      description="The portion of the overall spot fluorescence contributed by channel Cy3 (normalized so that channel Cy3 contribution equals 1)."
     2185      column="cy3_ratio"
     2186      channel="1"
     2187      type="float"
     2188    />
     2189    <property
     2190      name="Cy3Percent"
     2191      title="Cy3 precent"
     2192      description="The portion of the overall spot fluorescence contributed by channel Cy3 (in percent)."
     2193      column="cy3_percent"
     2194      channel="1"
     2195      type="float"
     2196    />
     2197    <property
     2198      name="Cy3SignalNoiseRatioFilter"
     2199      title="Cy3 signal noise ratio filter"
     2200      description="Cy3 signal noise ratio filter"
     2201      column="cy3_snr_filter"
     2202      channel="1"
     2203      type="float"
     2204    />
     2205    <property
     2206      name="Cy5Ratio"
     2207      title="Cy5 ratio"
     2208      description="The portion of the overall spot fluorescence contributed by channel Cy5 (normalized so that channel Cy5 contribution equals 1)."
     2209      column="cy5_ratio"
     2210      channel="2"
     2211      type="float"
     2212    />
     2213    <property
     2214      name="Cy5Percent"
     2215      title="Cy5 precent"
     2216      description="The portion of the overall spot fluorescence contributed by channel Cy5 (in percent)."
     2217      column="cy5_percent"
     2218      channel="2"
     2219      type="float"
     2220    />
     2221    <property
     2222      name="Cy5SignalNoiseRatioFilter"
     2223      title="Cy5 signal noise ratio filter"
     2224      description="Cy5 signal noise ratio filter"
     2225      column="cy5_snr_filter"
     2226      channel="2"
     2227      type="float"
     2228    />
     2229    <property
     2230      name="log_normalised"
     2231      title="Normalized ratio"
     2232      description="Ratio = log2 Cy5 - log2 Cy3, for dyeswap ratio *-1"
     2233      column="log_normalised"
     2234      type="float"
     2235    />
     2236    <intensity-formula
     2237      name="meanfg"
     2238      title="Mean FG"
     2239      description="Mean foreground intensity"
     2240      >
     2241      <formula
     2242        channel="1"
     2243        expression="raw('Cy3Intensity')"
     2244      />
     2245      <formula
     2246        channel="2"
     2247        expression="raw('Cy5Intensity')"
     2248      />
     2249    </intensity-formula>
     2250    <intensity-formula
     2251      name="mean"
     2252      title="Mean FG - Mean BG"
     2253      description="Subtract mean background from mean foreground"
     2254      >
     2255      <formula
     2256        channel="1"
     2257        expression="raw('Cy3Intensity') - raw('Cy3Background')"
     2258      />
     2259      <formula
     2260        channel="2"
     2261        expression="raw('Cy5Intensity') - raw('Cy5Background')"
     2262      />
     2263    </intensity-formula>
    17592264  </raw-data-type>
    1760   -->
     2265 
    17612266  <raw-data-type
    17622267    id="spotfinder"
    … …  
    18782383      type="string"
    18792384    />
     2385    <intensity-formula
     2386      name="int"
     2387      title="Spot intensity"
     2388      description="Spot intensity corrected for background."
     2389      >
     2390      <formula
     2391        channel="1"
     2392        expression="raw('intA')"
     2393      />
     2394      <formula
     2395        channel="2"
     2396        expression="raw('intB')"
     2397      />
     2398    </intensity-formula>
    18802399  </raw-data-type>
    18812400</raw-data-types>
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