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Sample GSM48550 Query DataSets for GSM48550
Status Public on Apr 21, 2005
Title R-3-C2-1
Sample type RNA
 
Channel 1
Source name cy3 Liver5
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name cy5 Pool
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
13249 1747.34 859.908 0.1738 0.348116 0.617597 30.5182 0 1 1 30.5182 45.5364 12.0299 7.07257 2 0 0 0 58 58 461.828 215.207 460 216 11.8841 7.27591 267 267 389.903 202.161 390 202 4.00726 5.48754 0 0 0 0 0.285283 0.00027993 0 0 0 0 0 0 0 0 0 -1.4747 6.5201 1.57962 1.01268 0.26589 0 1 0.354273 1.19E-08 1 1 0 0 0 463.302 208.687 4.00726 5.48754 0 -11.2309 45.5364 12.0299 7.07257 0.26589 1
468 3776.57 1973.83 0.0563692 0.123304 0.64756 0 0 1 1 1818.58 2070.62 29.8621 45.3888 2 1 1 0 55 55 710.309 496.382 709 492 30.0893 46.4389 263 263 389.43 203.783 389 203 3.73269 5.446 0 0 0 0 0.320264 0.000663571 0 0 0 0 0 0 0 0 0 247.48 286.073 4.06376 6.27082 0.319293 1 1 1.06E-51 5.44E-45 1 1 1 1 0 462.829 210.309 3.73269 5.446 1 1818.58 2070.62 29.8621 45.3888 0.319293 1
8299 1851.59 1293.36 -0.116576 0.136208 0.392071 0 0 1 1 10536.1 8055.71 119.216 119.834 0 3 0 0 56 56 1902.21 1317.98 1896 1318.5 121.864 123.391 272 272 389.426 202.816 389 202.5 4.11663 5.04694 0 0 0 0 0.453403 0.000399828 0 0 0 0 0 0 0 0 0 1439.39 1108.64 16.2867 16.4917 0.453272 1 1 5.45E-61 1.61E-54 1 1 1 1 0 462.826 209.342 4.11663 5.04694 1 10536.1 8055.71 119.216 119.834 0.453272 1
21976 3610.52 91.6961 0.148222 0.119217 0.213758 0 0 1 1 8519.94 11985.6 101.677 177.263 1 0 0 0 57 57 1630.51 1858.4 1622 1833 104.997 183.912 264 264 391.557 204.67 391 205 4.32569 4.99518 0 0 0 0 0.551554 0.000488878 0 0 0 0 0 0 0 1 0 1165.55 1647.21 13.9097 24.3616 0.55141 1 1 1.40E-60 2.16E-55 1 1 1 1 0 464.956 211.196 4.32569 4.99518 1 8519.94 11985.6 101.677 177.263 0.55141 1
21053 393.348 180.818 1.18934 0.191854 5.67E-10 0 0 1 1 999.063 15450.3 24.4439 152.173 1 2 0 0 57 57 599.211 2362.28 598 2370 24.8242 160.053 268 268 390.996 203.082 391 203 4.29397 5.47182 0 0 0 0 0.160494 -4.93E-05 0 0 0 0 0 0 0 0 0 134.815 2152.67 3.29849 21.2021 0.159966 1 1 9.08E-44 3.28E-65 1 1 1 1 0 464.396 209.608 4.29397 5.47182 0 999.063 15450.3 24.4439 152.173 0.159966 1
22064 1748.24 88.3495 0.0624099 0.123221 0.612515 0 0 1 1 1144.87 1321.8 25.0669 23.4649 2 1 0 1 56 56 622.464 388.875 623.5 387 25.8963 23.7212 270 270 390.596 202.807 390 203 4.13031 5.46227 0 0 0 0 0.125207 0.000156236 0 0 0 0 0 0 0 0 0 158.468 179.542 3.46965 3.18726 0.124199 1 1 9.17E-46 3.80E-51 1 1 1 1 0 463.996 209.333 4.13031 5.46227 1 1144.87 1321.8 25.0669 23.4649 0.124199 1
15703 4414.01 639.072 -0.403288 0.17142 0.0186409 0 0 1 1 2900.34 1145.94 39.4101 30.0399 2 1 0 0 58 58 858.431 368.5 856 371 40.8768 31.4599 265 265 389.683 203.917 390 204 3.63452 5.22602 0 0 0 0 0.458213 -0.000182848 0 0 0 0 0 0 0 0 0 395.348 158.057 5.37203 4.14335 0.45644 1 1 2.36E-58 1.27E-42 1 1 1 1 0 463.083 210.443 3.63452 5.22602 0 2900.34 1145.94 39.4101 30.0399 0.45644 1
5184 4073.81 1559.89 0.00438697 0.126925 0.972428 0 0 1 1 986.385 996.399 28.1123 25.4823 1 2 0 0 61 61 600.82 343.213 600 347 30.7243 26.567 265 265 389.113 203.083 389 203 4.07068 5.25853 0 0 0 0 0.392941 0.000320863 0 0 0 0 0 0 0 0 0 138.307 133.604 3.94179 3.41686 0.390395 1 1 6.49E-42 6.07E-45 1 1 1 1 0 462.513 209.609 4.07068 5.25853 1 986.385 996.399 28.1123 25.4823 0.390395 1
11723 2190.86 993.246 0.183774 0.00830063 0 0 1 1 4282.53 1401.56 33.6805 22.3814 3 2 0 0 57 57 1043.14 404.86 1038 400 34.4002 23.3088 265 265 389.642 203.8 389 204 3.7583 5.60789 0 0 0 0 0.225403 0.000305869 0 0 0 0 0 0 0 0 0 580.099 194.534 4.56226 3.10649 0.223727 1 1 6.29E-71 1.55E-54 1 1 1 1 0 463.041 210.326 3.7583 5.60789 0 4282.53 1401.56 33.6805 22.3814 0.223727 1
21076 4457.12 167.672 -0.103617 0.136367 0.44735 0 0 1 1 713.144 561.773 18.5594 22.6645 1 1 0 0 58 58 567.034 284.31 567 283 20.3003 22.3593 267 267 390.768 204.562 390 205 4.05489 5.35356 0 0 0 0 0.0290804 0.000181502 0 0 0 0 0 0 0 0 0 102.867 73.2228 2.67709 2.95414 0.0287785 1 1 5.99E-43 1.08E-32 1 1 1 1 0 464.167 211.088 4.05489 5.35356 0 713.144 561.773 18.5594 22.6645 0.0287785 1
22057 1896.17 89.852 -0.230634 0.148576 0.120593 0 0 1 1 2162.41 1271.47 41.9908 26.3377 0 0 0 1 61 61 760.262 385.344 758 388 44.7776 28.1679 263 263 391.312 203.916 391 204 4.24553 5.59654 0 0 0 0 0.0634072 0.000234457 0 0 0 0 0 0 0 0 0 295.551 174.902 5.73915 3.623 0.0630543 1 1 1.61E-51 2.27E-50 1 1 1 1 0 464.711 210.442 4.24553 5.59654 0 2162.41 1271.47 41.9908 26.3377 0.0630543 1
18963 3673.56 356.089 0.0163825 0.125615 0.896235 0 0 1 1 2559.64 2658.04 38.0944 64.1576 0 0 0 0 60 60 810.1 579.617 814.5 573.5 39.9027 68.9665 268 268 390.164 203.963 390 204 4.06261 5.42833 0 0 0 0 0.451983 0.000336901 0 0 0 0 0 0 0 0 0 346.536 369.128 5.15739 8.90971 0.451148 1 1 1.20E-57 2.09E-45 1 1 1 1 0 463.564 210.488 4.06261 5.42833 1 2559.64 2658.04 38.0944 64.1576 0.451148 1
2407 3692.2 1804.41 0.103443 0.156172 0.507737 0 0 1 1 109.983 139.563 13.7608 10.1209 0 2 0 0 56 56 478.946 228.357 476.5 229 14.9793 9.40489 268 268 389.437 203.918 389.5 204 3.87826 5.38141 0 0 0 0 0.297106 -5.99E-05 0 0 0 0 0 0 0 0 0 16.1102 17.9135 2.01566 1.29906 0.285443 1 1 7.45E-11 1.18E-20 1 1 1 1 0 462.836 210.444 3.87826 5.38141 1 109.983 139.563 13.7608 10.1209 0.285443 1
1400 2252.68 1895.63 -0.0255595 0.133823 0.84853 0 0 1 1 336.928 317.671 14.1299 12.5178 0 0 0 0 61 61 513.459 250.033 508 247 16.2774 12.0443 270 270 389.959 203.341 390 204 4.37828 5.85534 0 0 0 0 0.0193048 1.38E-05 0 0 0 0 0 0 0 0 0 50.1001 40.1663 2.10107 1.58275 0.0186577 1 1 6.40E-33 6.19E-36 1 1 1 1 0 463.359 209.866 4.37828 5.85534 1 336.928 317.671 14.1299 12.5178 0.0186577 1
13522 519.391 839.094 0.0351261 0.124865 0.77847 0 0 1 1 1050.53 1139.02 29.3839 23.7864 0 0 0 1 58 58 610.086 363.293 605.5 360.5 31.123 24.3015 277 277 390.285 203.101 390 203 4.33409 5.66363 0 0 0 0 0.201445 5.60E-05 0 0 0 0 0 0 0 0 0 146.401 153.666 4.09494 3.20903 0.199905 1 1 5.93E-41 1.65E-48 1 1 1 1 0 463.685 209.627 4.33409 5.66363 1 1050.53 1139.02 29.3839 23.7864 0.199905 1
10028 1661.48 1142.59 -0.123893 0.138593 0.371357 0 0 1 1 654.688 492.2 24.437 17.3161 0 0 0 0 60 60 559.783 272.517 560.5 270 27.4115 17.1548 270 270 391.3 202.274 391 201 4.43822 5.69475 0 0 0 0 0.0426654 0.000130632 0 0 0 0 0 0 0 0 0 95.0837 63.7168 3.54911 2.24163 0.0420317 1 1 5.74E-35 3.09E-37 1 1 1 1 0 464.7 208.8 4.43822 5.69475 0 654.688 492.2 24.437 17.3161 0.0420317 1
22540 774.465 49.5031 0.117646 0.120321 0.328192 0 0 1 1 3237.07 4244.22 52.8622 83.4557 0 0 0 1 59 59 902.085 800.356 895 788 54.7859 89.2271 275 275 391.644 202.796 391 203 4.19205 5.84052 0 0 0 0 0.412795 0.000364281 0 0 0 0 0 0 0 0 0 437.041 591.034 7.13699 11.6217 0.412347 1 1 1.66E-54 7.06E-50 1 1 1 1 0 465.043 209.322 4.19205 5.84052 1 3237.07 4244.22 52.8622 83.4557 0.412347 1
6752 2740.42 1427 -0.319079 0.159749 0.045785 0 0 1 1 2031.05 974.187 36.7852 27.9383 0 0 0 0 60 60 741.883 342.917 738.5 344 39.1456 29.4908 257 257 389.21 203.187 389 203 3.36843 5.02223 0 0 0 0 0.163165 -1.09E-05 0 0 0 0 0 0 0 0 0 279.274 133.204 5.05804 3.82011 0.162475 1 1 1.26E-52 1.92E-41 1 1 1 1 0 462.61 209.713 3.36843 5.02223 0 2031.05 974.187 36.7852 27.9383 0.162475 1
18604 2170.92 390.192 0.0457564 0.124668 0.7136 0 0 1 1 765.346 850.383 22.2555 19.6416 1 3 0 0 59 59 572.797 322.136 574 323 24.2044 19.8037 269 269 390.684 203.052 390 203 4.14393 5.48038 0 0 0 0 -0.0974538 0.000209148 0 0 0 0 0 0 0 0 0 108.713 112.558 3.16126 2.59979 -0.0963342 1 1 1.28E-40 6.12E-47 1 1 1 1 0 464.084 209.578 4.14393 5.48038 1 765.346 850.383 22.2555 19.6416 -0.0963342 1
16228 2403.15 598.473 0.141394 0.162952 0.385557 0 0 1 1 93.7413 129.815 11.7938 11.1521 3 2 0 0 54 54 476.63 226.463 475.5 225 12.5537 10.3116 274 274 389.533 203.234 389 203 3.74567 4.96842 0 0 0 0 0.245053 3.44E-05 0 0 0 0 0 0 0 0 0 13.6971 16.7036 1.72327 1.43497 0.237559 1 1 1.07E-10 8.42E-17 1 1 1 1 0 462.933 209.759 3.74567 4.96842 1 93.7413 129.815 11.7938 11.1521 0.237559 1

Total number of rows: 21446

Table truncated, full table size 8108 Kbytes.




Supplementary data files not provided

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