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Sample GSM47442 Query DataSets for GSM47442
Status Public on Apr 21, 2005
Title D-6-8
Sample type RNA
 
Channel 1
Source name cy3 Liver5
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name cy5 Liver3
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 05, 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 33.9048 32.7325 -1.50283 0.124273 1.14998e-033 0 0 1 1 11914.6 374.323 116.595 12.2994 1 3 4 0 55 55 1932.89 409.6 1942 407 113.126 22.0593 268 268 287.123 299.672 287 300 4.16015 6.52196 0 0 0 0 0.197584 -5.99634e-007 0 0 0 0 0 0 0 0 0 1558.98 91.3347 15.256 3.00104 0.195808 1 1 1.63444e-063 1.68203e-036 1 1 1 1 0 373.906 318.265 4.16015 6.52196 0 11914.6 374.323 116.595 12.2994 0.195808 1
2 54.4864 32.9151 -0.53214 0.277427 0.0550947 0 0 1 1 98.572 28.9477 12.327 6.44963 3 2 0 0 57 57 385.719 325.702 388 325 11.3117 12.262 282 282 286.706 299.66 286 299 5.16303 5.72729 0 0 0 0 -0.0401383 2.45164e-006 0 0 0 0 0 0 0 0 0 12.2306 7.44855 1.5295 1.65956 -0.0384797 1 1 4.56026e-011 3.24424e-005 1 1 0 0 0 373.489 318.253 5.16303 5.72729 0 98.572 28.9477 12.327 6.44963 -0.0384797 1
3 76.0608 32.1086 0.00813837 0.0522464 0.876215 0 0 1 1 856.921 873.13 22.0697 19.1896 8 6 1 0 53 53 487.755 527.057 490 525 21.3361 33.3204 284 284 286.609 299.588 286 300 4.94193 5.98136 0 0 0 0 0.384865 0.000306964 0 0 0 0 0 0 0 0 0 114.362 208.875 2.94537 4.59065 0.381809 1 1 1.23584e-040 6.20121e-044 1 1 1 1 0 373.392 318.182 4.94193 5.98136 1 856.921 873.13 22.0697 19.1896 0.381809 1
4 96.9928 32.4679 0.00748412 0.0726818 0.917986 0 0 1 1 284.246 289.187 15.9258 12.9862 6 8 1 0 51 51 411.706 386.392 409 385 15.317 21.6288 291 291 286.271 299.9 286 300 5.10157 6.00692 0 0 0 0 0.259948 0.000110155 0 0 0 0 0 0 0 0 0 38.6513 67.8982 2.16556 3.04903 0.255736 1 1 8.11061e-024 4.75748e-028 1 1 1 1 0 373.055 318.494 5.10157 6.00692 1 284.246 289.187 15.9258 12.9862 0.255736 1
5 119.921 33.6507 -0.0385849 0.0493818 0.434592 0 0 1 1 3963.49 3626.54 42.1662 47.6474 0 2 3 1 55 55 889.818 1206.84 891 1204 40.7054 86.4934 267 267 286.333 300.105 286 300 4.93542 6.14825 0 0 0 0 0.50454 0.000293102 0 0 0 0 0 0 0 0 0 516.702 888.138 5.49702 11.6688 0.503517 1 1 7.88508e-062 1.02901e-056 1 1 1 1 0 373.116 318.698 4.93542 6.14825 1 3963.49 3626.54 42.1662 47.6474 0.503517 1
6 139.289 32.8212 -0.0418319 0.0492751 0.395911 0 0 1 1 7612.76 6913.7 79.5727 78.9271 2 4 2 2 56 56 1362.55 2016.52 1371 2029.5 77.3713 145.039 269 269 286.204 299.844 286 300 4.88974 6.27345 0 0 0 0 0.736495 -4.90231e-005 0 0 0 0 0 0 0 0 0 989.566 1698.08 10.3435 19.3854 0.736045 1 1 6.22789e-063 8.55819e-061 1 1 1 1 0 372.988 318.437 4.88974 6.27345 1 7612.76 6913.7 79.5727 78.9271 0.736045 1
7 160.588 32.8713 -1.71226 0.139806 1.73433e-034 0 0 1 1 12366.6 239.875 141.963 11.0129 1 5 4 0 50 50 1997.56 376.94 1992 375.5 131.775 18.7338 275 275 287.175 300.015 287 299 4.9544 6.48523 0 0 0 0 -0.284426 -0.000141138 0 0 0 0 0 0 0 0 0 1623.6 58.3318 18.6382 2.67807 -0.281341 1 1 2.04802e-055 1.54494e-027 1 1 1 1 0 373.958 318.608 4.9544 6.48523 0 12366.6 239.875 141.963 11.0129 -0.281341 1
8 181.849 32.312 0.0336369 0.0751462 0.654428 0 0 1 1 259.976 280.912 17.8545 11.8485 4 5 2 0 54 54 408.667 383.907 405.5 381.5 17.6891 20.3045 277 277 286.581 299.267 286 299 4.8107 5.90266 0 0 0 0 0.446697 -0.000235849 0 0 0 0 0 0 0 0 0 35.3024 66.0466 2.42448 2.78577 0.439899 1 1 1.94429e-020 1.79775e-030 1 1 1 1 0 373.364 317.861 4.8107 5.90266 1 259.976 280.912 17.8545 11.8485 0.439899 1
9 202.737 32.8792 -0.00698432 0.0835301 0.933363 0 0 1 1 229.146 225.49 17.0086 12.8483 9 6 1 0 52 52 404.654 370.192 406.5 367 16.4244 21.7581 275 275 286.927 298.287 287 298 4.91034 5.82102 0 0 0 0 0.368849 -0.000133839 0 0 0 0 0 0 0 0 0 30.9435 53.3114 2.29682 3.03765 0.363319 1 1 1.04064e-018 1.36209e-023 1 1 1 1 0 373.71 316.881 4.91034 5.82102 1 229.146 225.49 17.0086 12.8483 0.363319 1
10 223.985 32.3232 0.0243211 0.0601977 0.686198 0 0 1 1 429.815 454.571 19.6383 16.7121 8 7 0 0 51 51 432 424.471 435 420 18.9631 27.8936 277 277 286.744 299.199 287 299 4.90297 5.90691 0 0 0 0 0.55854 -1.89248e-005 0 0 0 0 0 0 0 0 0 58.4732 106.678 2.67166 3.92198 0.552857 1 1 1.16408e-027 5.88321e-032 1 1 1 1 0 373.527 317.792 4.90297 5.90691 1 429.815 454.571 19.6383 16.7121 0.552857 1
11 245.159 32.9016 0.022572 0.0558367 0.686029 0 0 1 1 565.081 595.227 16.4597 13.2112 2 2 2 0 58 58 449.828 458.483 451 457.5 16.7878 23.6259 281 281 286.673 299.281 287 299 5.01636 5.703 0 0 0 0 0.290468 0.000256726 0 0 0 0 0 0 0 0 0 76.3719 140.608 2.22456 3.12083 0.286117 1 1 9.55992e-041 4.75089e-047 1 1 1 1 0 373.456 317.875 5.01636 5.703 1 565.081 595.227 16.4597 13.2112 0.286117 1
12 266.711 33.0322 0.028543 0.0654214 0.662623 0 0 1 1 344.327 367.718 14.897 13.263 5 6 1 0 53 53 420.906 404.132 420 403 14.6554 22.4474 280 280 287.182 299.421 287 299 4.48562 6.27399 0 0 0 0 0.378195 -6.61778e-005 0 0 0 0 0 0 0 0 0 46.9404 86.117 2.03084 3.1061 0.372143 1 1 1.24945e-029 1.94694e-033 1 1 1 1 0 373.965 318.015 4.48562 6.27399 1 344.327 367.718 14.897 13.263 0.372143 1
13 287.837 33.0984 -0.0179447 0.0495261 0.717107 0 0 1 1 2580.8 2476.34 33.1959 24.0744 4 3 2 0 56 56 711.804 922.589 708.5 922 32.3854 43.9337 277 277 287.794 298.942 288 299 4.88241 6.06758 0 0 0 0 0.225386 -0.000147601 0 0 0 0 0 0 0 0 0 337.226 605.053 4.33761 5.8822 0.224437 1 1 2.43424e-058 5.75157e-065 1 1 1 1 0 374.577 317.536 4.88241 6.06758 1 2580.8 2476.34 33.1959 24.0744 0.224437 1
14 308.756 33.3762 -1.62345 0.133135 3.34535e-034 0 0 1 1 15351.2 365.34 146.163 21.3708 2 10 2 0 48 48 2380.6 407.229 2386 399.5 132.347 36.0781 276 276 287.29 299.399 287 300 4.6165 6.01216 0 0 0 0 0.323676 0.000290569 0 0 0 0 0 0 0 0 0 2006.53 89.237 19.1047 5.21998 0.322863 1 1 1.97066e-057 6.45817e-022 1 1 1 1 0 374.073 317.992 4.6165 6.01216 0 15351.2 365.34 146.163 21.3708 0.322863 1
15 329.382 33 -0.115907 0.0797247 0.145992 0 0 1 1 281.218 215.346 14.471 9.47834 2 4 0 0 57 57 411.877 369.281 412 368 14.6471 16.6248 283 283 287.011 299.919 287 300 4.6574 6.39124 0 0 0 0 0.441026 0.000494725 0 0 0 0 0 0 0 0 0 38.0835 50.7683 1.95971 2.23454 0.430258 1 1 3.77725e-027 5.62705e-031 1 1 1 1 0 373.794 318.512 4.6574 6.39124 0 281.218 215.346 14.471 9.47834 0.430258 1
16 351.09 32.8404 -0.137794 0.101818 0.17595 0 0 1 1 202.229 147.248 15.6609 9.72945 4 9 0 0 54 54 400.704 352.963 399.5 351 15.1827 16.9483 288 288 286.997 299.059 287 299 4.75863 5.9808 0 0 0 0 0.159218 0.000135205 0 0 0 0 0 0 0 0 0 26.9241 35.3103 2.08504 2.33314 0.155964 1 1 2.77285e-018 2.37063e-021 1 1 1 1 0 373.78 317.653 4.75863 5.9808 1 202.229 147.248 15.6609 9.72945 0.155964 1
17 372.178 33.2186 0.0115198 0.0557187 0.836206 0 0 1 1 576.976 592.485 16.8365 13.9065 4 5 0 0 58 58 451.897 458.379 452 454.5 17.1625 24.8743 276 276 287.156 299.786 287 300 5.16009 5.9892 0 0 0 0 0.379282 0.000344972 0 0 0 0 0 0 0 0 0 77.9577 139.999 2.27485 3.28599 0.373467 1 1 9.87717e-041 1.10455e-045 1 1 1 1 0 373.939 318.38 5.16009 5.9892 1 576.976 592.485 16.8365 13.9065 0.373467 1
18 393.34 32.9656 -0.0695792 0.0527101 0.186823 0 0 1 1 903.473 769.725 18.1017 17.2835 5 5 0 0 53 53 494.057 501.887 492 497 17.4845 29.9645 282 282 286.582 299.333 286 300 4.72994 5.85065 0 0 0 0 0.532358 0.00035904 0 0 0 0 0 0 0 0 0 120.692 183.96 2.41814 4.13066 0.526854 1 1 1.62967e-046 1.58367e-043 1 1 1 1 0 373.365 317.927 4.72994 5.85065 1 903.473 769.725 18.1017 17.2835 0.526854 1
19 414.886 33.6894 -0.0136132 0.0493076 0.782482 0 0 1 1 3896.32 3776.08 88.3001 80.0054 8 11 0 0 49 49 881.265 1242.9 865 1213 80.5475 137.136 278 278 286.565 299.493 287 299 4.97079 6.1993 0 0 0 0 0.705408 -0.000160714 0 0 0 0 0 0 0 0 0 507.917 924.812 11.5107 19.5944 0.705044 1 1 1.49979e-040 6.62271e-042 1 1 1 1 0 373.348 318.086 4.97079 6.1993 1 3896.32 3776.08 88.3001 80.0054 0.705044 1
20 435.885 33.0682 0.111912 0.0947048 0.237329 0 0 1 1 167.12 216.243 11.5893 9.85529 1 5 3 0 55 55 396.091 370.273 398 370 11.3256 17.1879 287 287 286.934 300.111 287 300 4.64538 6.60696 0 0 0 0 0.353282 0.000100474 0 0 0 0 0 0 0 0 0 22.374 51.5676 1.55157 2.3502 0.342903 1 1 9.28999e-021 1.67098e-029 1 1 1 1 0 373.717 318.705 4.64538 6.60696 0 167.12 216.243 11.5893 9.85529 0.342903 1

Total number of rows: 22493

Table truncated, full table size 8699 Kbytes.




Supplementary data files not provided

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