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agilentmicroarraydatatable [2013/06/09 18:07] (現在)
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 +=====Agilentマイクロアレイのデータ=====
 +  *[[http://​www.ncbi.nlm.nih.gov/​projects/​geo/​query/​acc.cgi?​acc=GSM76691|NCBI GEO Accession viewerのページを元に作成]]
 +
 +^ID_REF |Feature number|
 +^PositionX |Found X coordinate of feature centroid in pixels|
 +^PositionY |Found Y coordinate of feature centroid in pixels|
 +^VALUE |log(REDsignal/​GREENsignal) per feature (processed signals used)|
 +^LogRatioError |error of the log ratio calculated according to the error model chosen|
 +^PValueLogRatio |Significance level of the Log Ratio computed for a feature|
 +^gSurrogateUsed |The green surrogate value used|
 +^rSurrogateUsed |The red surrogate value used|
 +^gIsFound |A boolean used to flag found (strong) features.The flag is applied independently in each channel. A feature is considered found if the found spot centroid is within the bounds of the spot deviation limit with respect to corresponding nominal centroid.|
 +^rIsFound |A boolean used to flag found (strong) features.The flag is applied independently in each channel. A feature is considered found if the found spot centroid is within the bounds of the spot deviation limit with respect to corresponding nominal centroid.|
 +^gProcessedSignal |Dye-normalized signal after surrogate algorithm, green channel, used for computation of log ratio|
 +^rProcessedSignal |Dye-normalized signal after surrogate algorithm, red channel, used for computation of log ratio|
 +^gProcessedSigError |Standard error of propagated feature signal, green channel|
 +^rProcessedSigError |Standard error of propagated feature signal, red channel|
 +^gNumPixOLHi |Number of outlier pixels per feature with intensity > upper threshold set via the pixel outlier rejection method. The number is computed independently in each channel. These pixels are omitted from all subsequent calculations.|
 +^rNumPixOLHi |Number of outlier pixels per feature with intensity > upper threshold set via the pixel outlier rejection method. The number is computed independently in each channel. These pixels are omitted from all subsequent calculations.|
 +^gNumPixOLLo |Number of outlier pixels per feature with intensity < lower threshold set via the pixel outlier rejection method. The number is computed independently in each channel. NOTE: The pixel outlier method is the ONLY step that removes data in Feature Extraction.|
 +^rNumPixOLLo |Number of outlier pixels per feature with intensity < lower threshold set via the pixel outlier rejection method. The number is computed independently in each channel. NOTE: The pixel outlier method is the ONLY step that removes data in Feature Extraction.|
 +^gNumPix |Total number of pixels used to compute feature statistics; ie.total number of inlier pixels/per spot; same in both channels|
 +^rNumPix |Total number of pixels used to compute feature statistics; ie.total number of inlier pixels/per spot; same in both channels|
 +^gMeanSignal |Raw mean signal of feature in green channel (inlier pixels)|
 +^rMeanSignal |Raw mean signal of feature in red channel (inlier pixels)|
 +^gMedianSignal |Raw median signal of feature in green channel (inlier pixels)|
 +^rMedianSignal |Raw median signal of feature in red channel (inlier pixels)|
 +^gPixSDev |Standard deviation of all inlier pixels per feature; this is computed independently in each channel|
 +^rPixSDev |Standard deviation of all inlier pixels per feature; this is computed independently in each channel|
 +^gBGNumPix |Total Number of pixels used to compute Local BG statistics per spot; ie.total number of BG inlier pixels; same in both channels|
 +^rBGNumPix |Total Number of pixels used to compute Local BG statistics per spot; ie.total number of BG inlier pixels; same in both channels|
 +^gBGMeanSignal |Mean local background signal (local to corresponding feature) computed per channel (inlier pixels)|
 +^rBGMeanSignal |Mean local background signal (local to corresponding feature) computed per channel (inlier pixels)|
 +^gBGMedianSignal |Median local background signal (local to corresponding feature) computed per channel (inlier pixels)|
 +^rBGMedianSignal |Median local background signal (local to corresponding feature) computed per channel (inlier pixels)|
 +^gBGPixSDev |Standard deviation of all inlier pixels per Local BG of each feature, computed independently in each channel|
 +^rBGPixSDev |Standard deviation of all inlier pixels per Local BG of each feature, computed independently in each channel|
 +^gNumSatPix |Total number of saturated pixels per feature, computed per channel|
 +^rNumSatPix |Total number of saturated pixels per feature, computed per channel|
 +^gIsSaturated |Boolean flag indicating if a feature is saturated or not|
 +^rIsSaturated |Boolean flag indicating if a feature is saturated or not|
 +^PixCorrelation |Ratio of estimated feature covariance in RedGreen space to product of feature Standard Deviation in Red Green space.|
 +^BGPixCorrelation |Ratio of estimated background covariance in RedGreen space to product of background Standard Deviation in Red Green space.|
 +^gIsFeatNonUnifOL |Boolean flag indicating if a feature is NonUniformity Outlier or not Green Channel|
 +^rIsFeatNonUnifOL |Boolean flag indicating if a feature is NonUniformity Outlier or not Red Channel|
 +^gIsBGNonUnifOL |Boolean flag indicating if background is NonUniformity Outlier or not Green Channel|
 +^rIsBGNonUnifOL |Boolean flag indicating if background is NonUniformity Outlier or not Red Channel|
 +^gIsFeatPopnOL |Boolean flag indicating if a feature is a Population Outlier or not for Green Channel. Probes with replicate features on a microarray are examined using population statistics|
 +^rIsFeatPopnOL |Boolean flag indicating if a feature is a Population Outlier or not for Red Channe. Probes with replicate features on a microarray are examined using population statistics|
 +^gIsBGPopnOL |Boolean flag indicating if background is a Population Outlier or not for Green Channel.|
 +^rIsBGPopnOL |Boolean flag indicating if background is a Population Outlier or not for Red Channel.|
 +^IsManualFlag |Manual Flag|
 +^gBGSubSignal |The net g signal following the subtraction of the background from the raw mean g signal|
 +^rBGSubSignal |The net r signal following the subtraction of the background from the raw mean r signal|
 +^gBGSubSigError |Propagated standard error as computed on net g background subtracted signal|
 +^rBGSubSigError |Propagated standard error as computed on net r background subtracted signal|
 +^BGSubSigCorrelation |Ratio of estimated background subtracted feature signal covariance in RG space to product of background subtracted feature Standard Deviation in RG space|
 +^gIsPosAndSignif |Boolean flag indicating if the mean signal of a feature is greater than the corresponding background (selected by user) and if this difference is significant|
 +^rIsPosAndSignif |Boolean flag indicating if the mean signal of a feature is greater than the corresponding background (selected by user) and if this difference is significant|
 +^gPValFeatEqBG |P-value from t-test of significance between g Mean signal and g background (selected by user)|
 +^rPValFeatEqBG |P-value from t-test of significance between r Mean signal and r background (selected by user)|
 +^gNumBGUsed |Number of local background regions or features used to calculate the background subtraction on this feature g channel.|
 +^rNumBGUsed |Number of local background regions or features used to calculate the background subtraction on this feature r channel.|
 +^gIsWellAboveBG |Boolean flag indicating if a feature is WellAbove Background or not|
 +^rIsWellAboveBG |Boolean flag indicating if a feature is WellAbove Background or not|
 +^IsUsedBGAdjust |A boolean used to flag features used for computation of global BG offset|
 +^gBGUsed |Background value (after global background adjust if turned ON) subtracted from the raw mean signal to generate the BG subtracted signal; this value is computed per channel. If global BG subtraction is used the column is identical for every feature in a given channel|
 +^rBGUsed |Background value (after global background adjust if turned ON) subtracted from the raw mean signal to generate the BG subtracted signal; this value is computed per channel. If global BG subtraction is used the column is identical for every feature in a given channel|
 +^gBGSDUsed |Standard deviation of background used in g channel|
 +^rBGSDUsed |Standard deviation of background used in r channel|
 +^IsNormalization |A boolean flag which indicates if a feature is used to measure dye bias|
 +^gDyeNormSignal |The dye-normalized signal in the indicated channel|
 +^rDyeNormSignal |The dye-normalized signal in the indicated channel|
 +^gDyeNormError |The standard error associated with the dye normalized signal|
 +^rDyeNormError |The standard error associated with the dye normalized signal|
 +^DyeNormCorrelation |Dye-normalized red and green pixel correlation|
 +^ErrorModel |Indicates the error model that you chose for Feature Extraction or that the software uses if you have chosen the "Most Conservative"​ option|
 +
 +
 +======リンク======
 +
 +  *[[AgilentMicroArrayDataTable]]
 +  *[[PerkinElmerMicroArrayDataTable]]
 +  *[[AgilentGenePix3DataTable]]
 +
 +