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Sample GSM47065 Query DataSets for GSM47065
Status Public on Apr 21, 2005
Title D-2-2
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 01, 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 GPL891
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
1 35.8843 37.955 -0.858099 0.0806619 1.97874e-026 0 0 1 1 6172.71 855.808 62.8532 32.9059 5 0 0 0 58 58 1112.79 93.9483 1097.5 94 78.8934 10.3473 267 267 38.1685 53.3745 38 54 3.52511 6.45183 0 0 0 0 -0.074501 -0.000146633 0 0 0 0 0 0 0 0 0 1017.58 36.7979 10.3615 1.41488 -0.0715266 1 1 2.48719e-065 1.0398e-036 1 1 1 1 0 95.2117 57.1504 3.52511 6.45183 0 6172.71 855.808 62.8532 32.9059 -0.0715266 1
2 56.4104 37.8806 0 0.0751589 1 0 121.547 1 1 73.662 121.547 7.77654 18.236 0 1 0 1 57 57 104.877 61.0526 105 61 7.8787 6.56131 278 278 37.7914 52.9388 38 53 3.12085 6.3194 0 0 0 0 0.129666 -0.000309176 0 0 0 0 0 1 0 0 0 10.0427 4.33792 1.06021 0.948118 0.116966 1 1 1.69137e-013 1.74616e-005 1 1 1 0 0 94.8345 56.7147 3.12085 6.3194 0 73.662 83.4351 7.77654 18.236 0.116966 0
3 78.2515 38.4728 -0.136024 0.0509193 0.00755452 0 0 1 1 2002.4 1463.95 17.0889 47.5388 0 0 0 0 58 58 420.862 119.966 424.5 119 21.1066 15.51 283 283 37.9399 52.4276 38 52 3.90034 6.28385 0 0 0 0 -0.146694 9.21628e-005 0 0 0 0 0 0 0 0 0 325.879 63.7621 2.78112 2.07054 -0.143784 1 1 2.03291e-070 7.88641e-039 1 1 1 1 0 94.9831 56.2034 3.90034 6.28385 0 2002.4 1463.95 17.0889 47.5388 -0.143784 1
4 99.6248 38.2161 0.0340605 0.0571191 0.55097 0 0 1 1 508.625 550.121 11.6059 33.6833 0 2 0 0 58 58 173.517 81.4138 174 82 13.6346 11.3122 287 287 37.439 52.5436 38 53 3.67979 6.65934 0 0 0 0 -0.165319 2.85929e-005 0 0 0 0 0 0 0 0 0 79.0351 25.0944 1.80344 1.5365 -0.158653 1 1 1.53393e-046 9.93204e-025 1 1 1 1 0 94.4821 56.3194 3.67979 6.65934 1 508.625 550.121 11.6059 33.6833 -0.158653 1
5 120.882 38.0967 -0.309988 0.05429 1.13079e-008 0 0 1 1 5045.67 2471.33 45.6098 47.7887 1 1 0 0 60 60 942.733 160.4 938.5 160.5 59.3904 15.3504 286 286 37.1399 52.4615 37 52 3.69751 6.09373 0 0 0 0 -0.0164274 -0.000130931 0 0 0 0 0 0 0 0 0 848.55 104.163 7.67038 2.01422 -0.0161565 1 1 3.27748e-070 2.74552e-053 1 1 1 1 0 94.183 56.2374 3.69751 6.09373 0 5045.67 2471.33 45.6098 47.7887 -0.0161565 1
6 141.995 37.6383 -0.535197 0.0630328 2.05254e-017 0 0 1 1 8727.39 2544.99 75.7951 54.5591 0 0 0 0 61 61 1589.49 161.23 1569 165 101.417 17.3881 279 279 37.147 52.1649 37 52 3.00178 6.21104 0 0 0 0 0.277375 -0.000123617 0 0 0 0 0 0 0 0 0 1495.3 105.289 12.9863 2.25716 0.273559 1 1 3.99061e-072 8.75277e-051 1 1 1 1 0 94.1901 55.9407 3.00178 6.21104 0 8727.39 2544.99 75.7951 54.5591 0.273559 1
7 162.165 38.4414 -1.32645 0.111663 1.52039e-032 0 0 1 1 7963.62 375.542 102.16 23.9878 0 1 0 0 57 57 1391.11 72.7895 1373 73 125.561 7.26473 282 282 37.5461 52.6631 38 52.5 3.34276 6.81818 0 0 0 0 0.0496709 -7.31547e-005 0 0 0 0 0 0 0 0 0 1296.52 16.3505 16.6322 1.04439 0.0457601 1 1 8.13208e-059 1.13168e-025 1 1 1 0 0 94.5892 56.439 3.34276 6.81818 0 7963.62 375.542 102.16 23.9878 0.0457601 1
8 183.236 37.4907 0.0750499 0.0525923 0.153577 0 0 1 1 784.269 932.213 12.034 36.778 4 0 2 1 51 51 219.196 97.098 220 97 13.6015 11.3987 287 287 37.3937 51.784 37 52 3.26804 6.29202 0 0 0 0 -0.159054 0.000114 0 0 0 0 0 0 0 0 0 124.759 41.5382 1.91434 1.63878 -0.154124 1 1 8.31514e-051 3.32085e-032 1 1 1 1 0 94.4369 55.5598 3.26804 6.29202 0 784.269 932.213 12.034 36.778 -0.154124 1
9 204.987 37.8589 0.121518 0.0750493 0.105409 0 0 1 1 237.489 314.168 7.46917 26.3076 4 0 0 0 59 59 130.525 70.339 131 70 8.53665 9.01457 284 284 37.6092 51.8204 37 52 3.27406 6.45447 0 0 0 0 0.150446 -3.11655e-005 0 0 0 0 0 0 0 0 0 35.8731 14.7427 1.12823 1.23451 0.140884 1 1 6.38283e-040 1.23614e-018 1 1 1 0 0 94.6523 55.5963 3.27406 6.45447 0 237.489 314.168 7.46917 26.3076 0.140884 1
10 226.789 38.0636 -0.128713 0.0613293 0.0358422 0 0 1 1 500.104 371.833 10.385 27.5216 0 1 0 0 62 62 170.871 73.2903 167.5 73.5 12.5037 9.47367 270 270 36.8111 52.4 37 52.5 3.12168 6.51187 0 0 0 0 0.0452989 0.000429011 0 0 0 0 0 0 0 0 0 77.0167 17.1145 1.5993 1.26674 0.0427363 1 1 2.84073e-051 9.38195e-022 1 1 1 1 0 93.8542 56.1759 3.12168 6.51187 0 500.104 371.833 10.385 27.5216 0.0427363 1
11 246.94 38.1725 0.0972149 0.0531863 0.0675769 0 0 1 1 717.961 898.081 11.2134 38.8105 1 0 0 0 62 62 208.274 95.6452 206.5 94 13.9038 13.3135 284 284 37.3803 51.7254 37 52 3.52925 6.54276 0 0 0 0 -0.0587132 -0.000123036 0 0 0 0 0 0 0 0 0 113.851 40.1439 1.77817 1.73482 -0.056829 1 1 7.33873e-059 7.8925e-034 1 1 1 1 0 94.4234 55.5012 3.52925 6.54276 0 717.961 898.081 11.2134 38.8105 -0.056829 1
12 268.249 38.0963 -0.0396826 0.0615615 0.519186 0 0 1 1 434.525 396.581 9.11856 24.6737 0 1 0 0 61 61 161.328 73.5246 160 74 10.8224 8.3877 279 279 37.4875 51.4624 37 51 3.53691 6.27297 0 0 0 0 0.188471 -0.000188209 0 0 0 0 0 0 0 0 0 66.7973 18.2864 1.40175 1.13771 0.175856 1 1 4.90945e-051 4.69176e-026 1 1 1 1 0 94.5306 55.2382 3.53691 6.27297 1 434.525 396.581 9.11856 24.6737 0.175856 1
13 288.943 38.2369 -0.0462188 0.0496359 0.351772 0 0 1 1 2622.26 2357.53 20.0822 51.9199 0 0 0 0 63 63 528.73 157.19 529 156 26.3152 17.3464 285 285 37.8737 52.4035 38 52 3.61309 7.01271 0 0 0 0 -0.18871 -0.000240622 0 0 0 0 0 0 0 0 0 433.813 101.011 3.32231 2.22457 -0.185008 1 1 6.53888e-078 8.40474e-052 1 1 1 1 0 94.9168 56.1794 3.61309 7.01271 1 2622.26 2357.53 20.0822 51.9199 -0.185008 1
14 310.546 38.2884 -1.2337 0.105144 8.59456e-032 0 0 1 1 8245.34 481.405 87.4432 29.4434 0 1 0 0 57 57 1445.4 76.4211 1413 77 108.106 9.23299 283 283 38.0141 51.8092 38 52 3.63198 6.02821 0 0 0 0 -0.0884621 -2.42474e-006 0 0 0 0 0 0 0 0 0 1350.35 20.836 14.3206 1.27436 -0.0848832 1 1 2.02519e-063 6.90556e-025 1 1 1 1 0 95.0573 55.585 3.63198 6.02821 0 8245.34 481.405 87.4432 29.4434 -0.0848832 1
15 332.199 38.7 0.464717 0.0612228 3.18465e-014 0 0 1 1 658.647 1920.3 11.6019 50.3042 0 2 0 0 59 59 200.712 140.373 200 142 14.2297 16.7897 276 276 37.7971 51.9167 38 52 3.55969 6.28102 0 0 0 0 -0.030141 0.000109212 0 0 0 0 0 0 0 0 0 105.872 84.6804 1.8649 2.21828 -0.0295012 1 1 1.45287e-053 1.53633e-044 1 1 1 1 0 94.8402 55.6925 3.55969 6.28102 0 658.647 1920.3 11.6019 50.3042 -0.0295012 1
16 353.209 38.2484 -0.39308 0.0617927 2.00089e-010 0 0 1 1 974.512 394.191 10.5636 33.5216 1 0 1 0 59 59 247 73.8305 247 73 12.5917 11.2956 276 276 37.4275 52.2029 37 52 3.57951 6.26118 0 0 0 0 -0.122554 -0.000192786 0 0 0 0 0 0 0 0 0 152.529 17.8517 1.6534 1.51809 -0.117711 1 1 2.24886e-066 7.92207e-018 1 1 1 1 0 94.4707 55.9788 3.57951 6.26118 0 974.512 394.191 10.5636 33.5216 -0.117711 1
17 373.963 38.8058 -0.00688249 0.0492887 0.888947 0 0 1 1 4010.34 3947.28 24.4918 58.0397 0 2 0 0 61 61 773.951 222.279 776 218 32.3442 18.7396 280 280 37.7607 53.2857 38 53 3.85813 6.3633 0 0 0 0 0.13663 0.000175268 0 0 0 0 0 0 0 0 0 679.147 165.217 4.14766 2.4293 0.134739 1 1 1.15681e-081 1.03218e-060 1 1 1 1 0 94.8038 57.0616 3.85813 6.3633 1 4010.34 3947.28 24.4918 58.0397 0.134739 1
18 395.107 37.5906 -0.26529 0.05415 9.62403e-007 0 0 1 1 1726.44 937.265 18.733 30.4313 0 2 0 1 56 56 372.946 98.4107 371.5 98 22.5642 9.48449 285 285 37.414 53.4491 37 53 3.34892 7.19852 0 0 0 0 -0.0225791 0.000295198 0 0 0 0 0 0 0 1 0 278.489 41.1857 3.02178 1.33722 -0.0213481 1 1 2.20259e-062 1.16407e-041 1 1 1 1 0 94.4572 57.225 3.34892 7.19852 0 1726.44 937.265 18.733 30.4313 -0.0213481 1
19 416.319 38.3839 0.124297 0.0500074 0.012934 0 0 1 1 6592.25 8776.7 66.8723 134.801 4 1 0 0 55 55 1278.07 402.364 1257 404 89.007 39.3669 285 285 37.7263 52.0035 38 51 3.52389 6.72629 0 0 0 0 0.550326 0.00023418 0 0 0 0 0 0 0 0 0 1183.3 346.584 12.0035 5.32317 0.5487 1 1 1.12222e-062 1.8868e-053 1 1 1 1 0 94.7694 55.7794 3.52389 6.72629 1 6592.25 8776.7 66.8723 134.801 0.5487 1
20 437.3 37.8589 0.169547 0.0507709 0.000839429 0 0 1 1 3987.67 5892.05 24.0306 86.8291 0 0 0 0 62 62 779.548 299.177 783 304 32.444 28.0605 279 279 37.7814 52.1756 37 52 3.68629 6.4167 0 0 0 0 -0.169374 0.000243489 0 0 0 0 0 0 0 0 0 684.724 243.226 4.1263 3.58434 -0.168156 1 1 4.20366e-083 3.33767e-060 1 1 1 1 0 94.8245 55.9515 3.68629 6.4167 1 3987.67 5892.05 24.0306 86.8291 -0.168156 1

Total number of rows: 22493

Table truncated, full table size 8715 Kbytes.




Supplementary data files not provided

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