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Sample GSM48552 Query DataSets for GSM48552
Status Public on Apr 21, 2005
Title R-3-C2-3
Sample type RNA
 
Channel 1
Source name cy3 Pool
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name cy5 Liver5
Organism Mus musculus
Extracted molecule total RNA
 
 
Description Each laboratory was provided with aliquots of two different RNA samples that were prepared in one of the Consortium laboratories - a sample prepared from mouse livers (Liver RNA), and a sample prepared from equal amounts of RNA isolated from five mouse tissues (liver, kidney, lung, brain and spleen: Pooled RNA).
 
Submission date Apr 19, 2005
Last update date May 27, 2005
Contact name Kenneth Lyon Phillips
E-mail(s) kphillips@icoria.com
Phone 919 425 3075
Organization name Paradigm Array Labs
Street address
City Research Triangle Park
State/province NC
ZIP/Postal code 27709
Country USA
 
Platform ID GPL922
Series (1)
GSE2458 Cross-platform comparability of microarray data

Data table header descriptions
ID_REF
PositionX Found coordinates of the feature centroid in pixels
PositionY Found coordinates of the feature centroid in pixels
VALUE (base 10) 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
rIsFound A boolean used to flag found (strong) features. The flag is applied independently in each channel
gProcessedSignal Dye-normalized signal after surrogate algorithm, per channel, used for computation of log ratio
rProcessedSignal Dye-normalized signal after surrogate algorithm, per channel, used for computation of log ratio
gProcessedSigError Standard error of propagated feature signal, per channel
rProcessedSigError Standard error of propagated feature signal, per channel
gNumPixOLHi Number of outlier pixels per feature with intensity > upper threshold set via the pixel outlier rejection method
rNumPixOLHi Number of outlier pixels per feature with intensity > upper threshold set via the pixel outlier rejection method
gNumPixOLLo Number of outlier pixels per feature with intensity < lower threshold set via the pixel outlier rejection method
rNumPixOLLo Number of outlier pixels per feature with intensity < lower threshold set via the pixel outlier rejection method
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 Median local background signal (local to corresponding feature) computed per channel (inlier pixels)
rMedianSignal Median local background signal (local to corresponding feature) computed per 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. A feature is saturated IF 50% of the pixels in a feature are above the saturation threshold
rIsSaturated Boolean flag indicating if a feature is saturated or not. A feature is saturated IF 50% of the pixels in a feature are above the saturation threshold
PixCorrelation Ratio of estimated feature covariance in RedGreen space to product of feature Standard Deviation in Red Green space
BGPixCorrelation The same concept as above but in case of background
gIsFeatNonUnifOL Boolean flag indicating if a feature is a NonUniformity Outlier or not. A feature is non-uniform if the pixel noise of feature exceeds a threshold established for a "uniform" feature
rIsFeatNonUnifOL Boolean flag indicating if a feature is a NonUniformity Outlier or not. A feature is non-uniform if the pixel noise of feature exceeds a threshold established for a "uniform" feature
gIsBGNonUnifOL The same concept as above but in case of background
rIsBGNonUnifOL The same concept as above but in case of background
gIsFeatPopnOL Boolean flag indicating if a feature is a Population Outlier or not. 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. Probes with replicate features on a microarray are examined using population statistics
gIsBGPopnOL The same concept as above but in case of background
rIsBGPopnOL The same concept as above but in case of background
IsManualFlag Boolean is manual flag
gBGSubSignal Background-subtracted signal
rBGSubSignal Background-subtracted signal
gBGSubSigError Propagated standard error as computed on net g(r) background subtracted signal
rBGSubSigError Propagated standard error as computed on net g(r) background subtracted signal
BGSubSigCorrelation Ratio of estimated background-subtracted feature signal co-variance in RG space to product of background-subtracted feature Standard Deviation in RG space
gIsPosAndSignif Boolean flag, established via a 2-sided t-test, indicates 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, established via a 2-sided t-test, indicates 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(r) Mean signal and g(r) background (selected by user)
rPValFeatEqBG P-value from t-test of significance between g(r) Mean signal and g(r) background (selected by user)
gNumBGUsed Background used to subtract from the MeanSignal; variable also used in t-test
rNumBGUsed Background used to subtract from the MeanSignal; variable also used in t-test
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 Boolean used to flag features used for computation of global BG offset
gBGUsed Background used to subtract fromthe MeanSignal; variable also used in t-test
rBGUsed Background used to subtract fromthe MeanSignal; variable also used in t-test
gBGSDUsed Standard deviation of background used in g(r) channel; variable also used in t-test and surrogate algorithms
rBGSDUsed Standard deviation of background used in g(r) channel; variable also used in t-test and surrogate algorithms
IsNormalization 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

Data table
ID_REF PositionX PositionY VALUE LogRatioError PValueLogRatio gSurrogateUsed rSurrogateUsed gIsFound rIsFound gProcessedSignal rProcessedSignal gProcessedSigError rProcessedSigError gNumPixOLHi rNumPixOLHi gNumPixOLLo rNumPixOLLo gNumPix rNumPix gMeanSignal rMeanSignal gMedianSignal rMedianSignal gPixSDev rPixSDev gBGNumPix rBGNumPix gBGMeanSignal rBGMeanSignal gBGMedianSignal rBGMedianSignal gBGPixSDev rBGPixSDev gNumSatPix rNumSatPix gIsSaturated rIsSaturated PixCorrelation BGPixCorrelation gIsFeatNonUnifOL rIsFeatNonUnifOL gIsBGNonUnifOL rIsBGNonUnifOL gIsFeatPopnOL rIsFeatPopnOL gIsBGPopnOL rIsBGPopnOL IsManualFlag gBGSubSignal rBGSubSignal gBGSubSigError rBGSubSigError BGSubSigCorrelation gIsPosAndSignif rIsPosAndSignif gPValFeatEqBG rPValFeatEqBG gNumBGUsed rNumBGUsed gIsWellAboveBG rIsWellAboveBG IsUsedBGAdjust gBGUsed rBGUsed gBGSDUsed rBGSDUsed IsNormalization gDyeNormSignal rDyeNormSignal gDyeNormError rDyeNormError DyeNormCorrelation ErrorModel
20847 213.145 183.235 1.07838 0.273955 8.27E-05 14.5689 0 1 1 14.5689 174.504 9.70386 18.7993 1 0 0 0 62 62 470.597 226.419 467 225 22.4064 12.4605 248 248 392.403 204.484 392 204 4.29182 5.24923 0 0 0 0 0.410165 3.23E-05 0 0 0 0 0 0 1 0 0 5.672 15.0117 2.85864 1.61721 0.399531 0 1 0.0516602 1.28E-13 1 1 0 1 0 464.925 211.408 4.29182 5.24923 0 19.254 174.504 9.70386 18.7993 0.399531 0
21060 254.686 164.374 0.998 0.249892 6.50E-05 17.1034 0 1 1 17.1034 170.248 8.13512 20.2888 5 2 0 0 56 56 471.321 226.482 467.5 224.5 17.7632 12.7821 245 245 393.045 204.906 393 205 5.03614 5.67524 0 0 0 0 0.561775 0.000746248 0 0 0 0 0 0 1 1 0 5.75498 14.6522 2.39541 1.74614 0.544572 0 1 0.0195609 1.05E-11 1 1 0 0 0 465.566 211.83 5.03614 5.67524 0 19.5446 170.248 8.13512 20.2888 0.544572 1
8098 1570.72 1289.57 0.988139 0.167606 3.73E-09 0 0 1 1 3382.16 32910.4 39.5524 330.748 1 1 0 0 57 57 1514.51 2891.26 1509 2873 92.8796 203.397 269 269 389.799 203.487 390 204 4.10095 5.14172 0 0 0 0 0.525916 0.000315301 0 0 0 0 0 0 0 0 0 1052.19 2680.85 12.3047 26.9424 0.525772 1 1 4.48E-61 1.04E-64 1 1 1 1 0 462.321 210.411 4.10095 5.14172 0 3382.16 32910.4 39.5524 330.748 0.525772 1
12526 3410.95 888.758 0.987048 0.167484 3.78E-09 0 0 1 1 2358.34 22890.4 36.5404 184.505 3 0 0 0 60 60 1199.07 2063.62 1190 2055 88.5326 115.735 258 258 388.69 202.616 389 203 4.13074 4.98988 0 0 0 0 0.365686 0.000195583 0 0 0 0 0 0 0 0 0 737.855 1854.08 11.4324 14.9445 0.365515 1 1 1.80E-56 4.27E-73 1 1 1 1 0 461.211 209.54 4.13074 4.98988 0 2358.34 22890.4 36.5404 184.505 0.365515 1
22343 403.394 50.9386 0.980743 0.26985 0.000278627 15.3095 0 1 1 15.3095 146.455 11.2884 24.8551 2 1 0 0 58 58 469.759 222.983 457.5 219 25.1007 16.1826 260 260 391.242 203.392 391 203 4.48581 5.24974 0 0 0 0 0.756173 0.000255569 0 0 0 0 0 0 0 0 0 5.99477 12.6666 3.30761 2.14968 0.744805 0 1 0.0751151 1.88E-07 1 1 0 0 0 463.764 210.316 4.48581 5.24974 0 20.4593 146.455 11.2884 24.8551 0.744805 0
9340 2585.96 1173.71 0.968163 0.165336 4.75E-09 0 0 1 1 2997.6 27857.1 30.169 215.066 0 0 0 0 61 61 1397.07 2471.26 1389 2476 73.52 136.349 264 264 388.871 202.697 388 203 4.3021 5.16119 0 0 0 0 0.512344 4.46E-05 0 0 0 0 0 0 0 0 0 935.673 2261.64 9.417 17.4606 0.512057 1 1 2.29E-68 3.37E-75 1 1 1 1 0 461.393 209.621 4.3021 5.16119 0 2997.6 27857.1 30.169 215.066 0.512057 1
7710 681.642 1329.53 0.95102 0.163412 5.89E-09 0 0 1 1 2307.16 20610.9 27.1774 230.946 1 0 0 1 56 56 1183.88 1880.45 1179 1879.5 63.5767 140.003 262 262 389.729 203.58 390 203 4.54849 5.54184 0 0 0 0 0.586009 0.000338336 0 0 0 0 0 0 0 0 0 721.624 1669.94 8.50045 18.7118 0.585591 1 1 4.08E-60 3.12E-61 1 1 1 1 0 462.251 210.504 4.54849 5.54184 0 2307.16 20610.9 27.1774 230.946 0.585591 1
19136 4573.57 302.575 0.941112 0.162303 6.69E-09 0 0 1 1 7041.05 61482.2 59.7979 596.631 2 1 0 0 55 55 2601.89 5336.05 2608 5268 134.777 368.917 254 254 389.307 202.894 389 203 3.95131 4.68204 0 0 0 0 0.653003 -0.000350512 0 0 0 0 0 0 0 0 0 2140.06 5126.24 18.175 49.7456 0.652931 1 1 8.17E-67 1.10E-63 1 1 1 1 0 461.829 209.818 3.95131 4.68204 1 7041.05 61482.2 59.7979 596.631 0.652931 1
18733 4002.12 341.811 0.930583 0.161138 7.69E-09 0 0 1 1 13576.6 115710 217.846 2280.52 1 0 0 0 62 62 4423.34 10259.7 4372.5 10267 500.56 1559.39 267 267 388.914 204.386 389 204 4.08142 5.35621 0 0 0 0 0.848353 0.000220837 0 1 0 0 0 0 0 0 0 3961.9 10048.4 63.5717 198.043 0.848346 1 1 6.06E-57 1.35E-51 1 1 1 1 0 461.435 211.31 4.08142 5.35621 0 13576.6 115710 217.846 2280.52 0.848346 1
640 154.428 1951.57 0.925927 0.160626 8.19E-09 0 0 1 1 22408 188943 151.252 1270.84 1 0 0 0 57 57 6719.89 17356.7 6682 17090 318.888 870.673 261 261 389.713 203.87 389 204 4.24058 5.4284 0 0 0 0 0.852886 0.000493071 0 0 0 0 0 0 0 0 0 6257.66 17145.9 42.2386 115.324 0.852866 1 1 2.40E-74 1.99E-74 1 1 1 1 0 462.234 210.794 4.24058 5.4284 1 22408 188943 151.252 1270.84 0.852866 1
9439 491.399 1179.21 0.923707 0.160387 8.45E-09 0 0 1 1 2872.68 24098.8 37.0886 315.497 4 0 0 0 54 54 1359.94 2163.31 1351 2108.5 85.1811 187.921 265 265 389.366 202.872 389 202 4.25223 5.56356 0 0 0 0 0.725953 -0.000232953 0 0 0 0 0 0 0 0 0 898.057 1953.52 11.5946 25.5751 0.725703 1 1 2.94E-56 6.52E-56 1 1 1 1 0 461.888 209.796 4.25223 5.56356 0 2872.68 24098.8 37.0886 315.497 0.725703 1
15963 3473.46 588.538 0.918233 0.159786 9.10E-09 0 0 1 1 4377.35 36261.4 46.3414 318.4 1 0 0 0 59 59 1815.42 3180.73 1849 3173 110.097 200.332 271 271 388.768 203.284 389 203 4.22179 5.68139 0 0 0 0 0.582723 0.000154926 0 0 0 0 0 0 0 0 0 1354.13 2970.52 14.3357 26.0832 0.582579 1 1 3.02E-65 6.42E-70 1 1 1 1 0 461.289 210.208 4.22179 5.68139 0 4377.35 36261.4 46.3414 318.4 0.582579 1
13535 256.959 822.887 0.914797 0.159412 9.55E-09 0 0 1 1 3520.81 28936.1 29.5597 255.5 4 0 2 2 57 57 1559.95 2565.04 1563 2586 69.4862 156.922 258 258 390.764 203.884 391 204 4.12951 5.29904 0 0 0 0 0.428638 0.000285269 0 0 0 0 0 0 0 0 0 1096.66 2354.23 9.20727 20.7874 0.428417 1 1 3.88E-69 7.40E-68 1 1 1 1 0 463.285 210.808 4.12951 5.29904 0 3520.81 28936.1 29.5597 255.5 0.428417 1
7069 597.428 1386.5 0.914443 0.15937 9.59E-09 0 0 1 1 46409.4 381108 306.084 3073.43 2 2 0 0 58 58 12672.3 36919.3 12575 36916.5 613.313 2254.48 272 272 389.25 204.563 389 204 4.30695 6.06452 0 0 0 0 0.877281 7.41E-05 0 0 0 0 0 0 0 0 0 12210.5 36707.8 80.5323 296.028 0.877276 1 1 5.36E-76 4.94E-71 1 1 1 1 0 461.772 211.486 4.30695 6.06452 1 46409.4 381108 306.084 3073.43 0.877276 1
6294 3348.77 1435.55 0.912805 0.1592 9.83E-09 0 0 1 1 2252.87 18430.7 26.9239 184.757 0 0 1 1 56 56 1166.71 1704.77 1166 1682.5 62.942 112.073 268 268 390.03 203.522 390 204 4.45525 5.16864 0 0 0 0 0.420618 0.00016557 0 0 0 0 0 0 0 0 0 704.163 1494.32 8.41538 14.9797 0.420305 1 1 9.08E-60 6.89E-64 1 1 1 1 0 462.551 210.446 4.45525 5.16864 0 2252.87 18430.7 26.9239 184.757 0.420305 1
4965 4174.54 1545.24 0.909934 0.158881 1.02E-08 0 0 1 1 9489.46 77121.6 107.304 953.609 0 0 5 2 52 52 3312.31 6718.42 3319 6750.5 232.365 580.292 247 247 390.069 203.397 390 204 3.18139 4.98906 0 0 0 0 0.708396 0.00024497 0 0 0 0 0 0 0 0 0 2849.72 6508.1 32.2238 80.4727 0.708376 1 1 1.73E-57 1.60E-55 1 1 1 1 0 462.59 210.321 3.18139 4.98906 1 9489.46 77121.6 107.304 953.609 0.708376 1
10987 4130.68 1018.68 0.907936 0.158669 1.05E-08 0 0 1 1 2798.26 22637.3 34.2776 150.912 1 1 0 0 61 61 1336.44 2044.84 1339 2050 83.7163 95.4652 272 272 388.702 203.765 389 204 3.67643 5.35008 0 0 0 0 0.282219 0.000438623 0 0 0 0 0 0 0 0 0 875.219 1834.15 10.7211 12.2274 0.282059 1 1 3.06E-63 4.62E-79 1 1 1 1 0 461.224 210.689 3.67643 5.35008 0 2798.26 22637.3 34.2776 150.912 0.282059 1
4206 2037.46 1626.54 0.896763 0.15746 1.23E-08 0 0 1 1 4911.86 38726.6 42.3362 310.357 1 1 0 0 58 58 1977.09 3392.71 1976.5 3392.5 99.4194 194.194 254 254 389.661 203.72 389 204 4.32608 5.47981 0 0 0 0 0.42788 -4.79E-05 0 0 0 0 0 0 0 0 0 1514.9 3182.06 13.0572 25.5013 0.427749 1 1 1.93E-69 3.30E-71 1 1 1 1 0 462.183 210.644 4.32608 5.47981 0 4911.86 38726.6 42.3362 310.357 0.427749 1
9626 1083.43 1158.57 0.890037 0.156738 1.36E-08 0 0 1 1 8681.46 67395.3 75.0492 524.39 0 1 0 0 57 57 3084.32 5864.95 3059 5816 171.119 332.185 265 265 389.804 203.057 390 203 3.95514 5.42795 0 0 0 0 0.705121 -1.07E-05 0 0 0 0 0 0 0 0 0 2621.99 5654.97 22.6665 44.0002 0.70506 1 1 2.35E-68 6.69E-71 1 1 1 1 0 462.325 209.98 3.95514 5.42795 1 8681.46 67395.3 75.0492 524.39 0.70506 1
13082 743.846 859.001 0.889213 0.156656 1.38E-08 0 0 1 1 2641.77 20469.5 21.5341 148.854 3 1 1 0 58 58 1288.6 1867.14 1288 1862.5 51.2787 91.7945 256 256 389.547 202.23 389 202 3.79444 4.7409 0 0 0 0 0.281736 0.000224584 0 0 0 0 0 0 0 0 0 826.535 1657.98 6.7374 12.0568 0.281477 1 1 6.57E-71 1.17E-73 1 1 1 1 0 462.068 209.154 3.79444 4.7409 0 2641.77 20469.5 21.5341 148.854 0.281477 1

Total number of rows: 21446

Table truncated, full table size 8103 Kbytes.




Supplementary data files not provided

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