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Sample GSM48641 Query DataSets for GSM48641
Status Public on Apr 21, 2005
Title R-8-C2-2
Sample type RNA
 
Channel 1
Source name cy3 Liver3
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 20, 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
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 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 -1.96709 0.159094 4.0756e-035 0 0 1 1 108747 1173.09 1498.65 17.2789 0 3 0 0 59 59 22777.6 665.949 22319 669 2372.43 35.2099 271 271 328.535 345.509 329 345 7.56733 9.34082 0 0 0 0 -0.402312 0.0001986 0 0 0 0 0 0 1 1 0 22412.2 313.585 308.865 4.61893 -0.399264 1 1 1.25976e-058 2.73423e-058 1 1 1 1 0 365.378 352.365 7.56733 9.34082 0 108747 1173.09 1498.65 17.2789 -0.399264 1
2 0 0.0879924 1 68.8277 21.7366 1 1 68.8277 21.7366 10.829 2.84993 0 1 1 0 57 57 362.439 354.912 362 354 9.2775 8.65258 288 288 325.531 341.399 326 340 8.4234 9.78498 0 0 0 0 0.0260697 0.000416265 0 0 0 0 0 0 0 1 0 0.0639776 6.65769 1.32529 1.28293 0.0216636 0 1 0.961625 1.36779e-006 1 1 0 0 0 362.375 348.255 8.4234 9.78498 0 0.522761 14.7895 10.829 2.84993 0.0216636 0
3 -0.130567 0.0502882 0.0094215 0 0 1 1 3654.2 2705.36 45.9873 26.789 1 4 0 0 56 56 1067.11 1122.73 1063 1112 66.1202 57.2133 280 280 327.179 341.232 326 341 7.86378 10.4037 0 0 0 0 0.605393 0.000176868 0 0 0 0 0 0 1 1 0 703.085 774.645 8.84817 7.67069 0.60255 1 1 1.05702e-058 8.31045e-065 1 1 1 1 0 364.022 348.087 7.86378 10.4037 0 3654.2 2705.36 45.9873 26.789 0.60255 1
4 0.0751337 0.0499117 0.132239 0 0 1 1 2055.21 2443.37 35.1956 38.2921 3 4 0 0 55 55 752.618 1057.8 741 1048 49.4891 82.2376 278 278 325.435 342.191 325 342 6.5363 10.7029 0 0 0 0 0.690168 -7.46349e-005 0 0 0 0 0 0 0 1 0 390.34 708.754 6.68461 11.1075 0.687828 1 1 9.65948e-051 8.47961e-053 1 1 1 1 0 362.279 349.046 6.5363 10.7029 1 2055.21 2443.37 35.1956 38.2921 0.687828 1
5 0.943814 0.0899964 9.88829e-026 0 0 1 1 156.91 1378.68 9.14503 18.0852 0 2 0 0 61 61 391.049 756.885 389 748 12.8094 41.7916 279 279 325.143 339.943 325 340 7.07012 9.24742 0 0 0 0 -0.122469 -0.000137981 0 0 0 0 0 0 0 1 0 29.0624 410.087 1.69382 5.37943 -0.117958 1 1 1.92394e-026 1.93759e-062 1 1 1 1 0 361.987 346.798 7.07012 9.24742 0 156.91 1378.68 9.14503 18.0852 -0.117958 1
6 0.405791 0.0583892 3.65918e-012 0 0 1 1 887.308 2258.73 12.8393 28.3422 2 1 0 0 57 57 530.719 1010.39 530 1008 17.8763 62.6951 287 287 327.383 340.341 327 340 7.52986 9.11821 0 0 0 0 0.360824 -0.000254906 0 0 0 0 0 0 1 1 0 166.493 663.189 2.40913 8.32159 0.353884 1 1 6.64216e-059 1.01184e-059 1 1 1 1 0 364.227 347.197 7.52986 9.11821 0 887.308 2258.73 12.8393 28.3422 0.353884 1
7 -2 0.160294 9.95921e-036 0 0 1 1 107701 196.537 1588.21 8.19323 0 3 0 0 60 60 21562.6 398.817 20940.5 396 2421.54 17.1953 278 278 326.104 336.953 326.5 337 7.57823 9.58835 0 0 0 0 -0.0300444 0.000126773 0 0 0 0 0 1 0 0 0 21199.7 55.0081 312.62 2.29318 -0.0290843 1 1 1.11323e-057 1.21989e-034 1 1 1 1 0 362.948 343.809 7.57823 9.58835 0 107701 196.537 1588.21 8.19323 -0.0290843 1
8 -0.290098 0.370952 0.434193 0 0 1 1 57.345 29.4034 9.3608 4.42254 1 0 0 0 58 58 369.897 350.966 369.5 352 11.1932 10.4495 282 282 323.613 334.27 324 334 7.77322 9.32252 0 0 0 0 -0.0529792 -0.000132459 0 0 0 0 0 0 0 0 0 9.43971 9.84073 1.54091 1.48014 -0.0468583 1 1 4.95053e-008 3.85913e-009 1 1 0 0 0 360.457 341.125 7.77322 9.32252 1 57.345 29.4034 9.3608 4.42254 -0.0468583 1
9 0 0.106603 1 69.3808 17.6949 1 1 69.3808 17.6949 14.2553 2.95711 0 0 0 1 57 57 359.351 347.421 359 346 11.2528 10.5288 284 284 324.081 333.373 324 333 7.57696 8.92656 0 0 0 0 0.160907 0.000380315 0 0 0 0 0 0 0 0 0 -1.57348 7.19253 1.5568 1.49178 0.144051 0 1 0.315816 7.5554e-006 1 1 0 0 0 360.924 340.229 7.57696 8.92656 0 -14.408 14.2575 14.2553 2.95711 0.144051 0
10 -0.226098 0.060096 0.000168374 0 0 1 1 648.003 385.016 10.7092 8.66552 0 1 0 0 59 59 479.559 455.186 480 456 14.9173 19.3502 278 278 322.701 333.802 323 334 6.71767 9.10511 0 0 0 0 0.243751 -0.000465049 0 0 0 0 0 0 0 0 0 120.015 114.529 1.98342 2.57769 0.233231 1 1 1.39441e-057 1.41901e-049 1 1 1 1 0 359.545 340.657 6.71767 9.10511 0 648.003 385.016 10.7092 8.66552 0.233231 1
11 -0.138344 0.0609824 0.0232928 0 0 1 1 517.064 376.011 12.3132 8.86468 0 0 0 0 61 61 455.902 450.754 455 450 17.5164 20.15 283 283 323.276 332.071 323 332 6.99202 9.13077 0 0 0 0 0.333543 -0.000185576 0 0 0 0 0 0 0 0 0 95.7827 111.828 2.28093 2.63642 0.320926 1 1 2.14793e-048 2.63432e-049 1 1 1 1 0 360.119 338.926 6.99202 9.13077 0 517.064 376.011 12.3132 8.86468 0.320926 1
12 0.0270037 0.0525163 0.607115 0 0 1 1 807.282 859.071 12.4526 12.6255 1 1 0 0 58 58 510.19 593.397 509 592 17.3796 28.2022 283 283 322.936 332.519 322 331 7.04113 7.96327 0 0 0 0 -0.0503025 0.00015383 0 0 0 0 0 0 0 0 0 150.41 254.022 2.32012 3.73327 -0.0490743 1 1 6.85569e-058 1.13155e-057 1 1 1 1 0 359.78 339.375 7.04113 7.96327 1 807.282 859.071 12.4526 12.6255 -0.0490743 1
13 -0.190405 0.0514476 0.0002148 0 0 1 1 3040.65 1961.38 29.5665 17.5312 1 0 0 1 60 60 940.35 908.3 941 907 43.4854 39.0663 267 267 324.352 334.127 324 334 7.27156 8.59263 0 0 0 0 0.480951 -0.000272439 0 0 0 0 0 0 0 0 0 579.155 567.317 5.63155 5.07078 0.476859 1 1 6.12798e-069 1.24768e-071 1 1 1 1 0 361.195 340.983 7.27156 8.59263 0 3040.65 1961.38 29.5665 17.5312 0.476859 1
14 -2 0.160676 1.44465e-035 0 0 1 1 108126 453.102 1200.32 8.99277 0 0 0 0 61 61 22284.4 465.918 21905 468 1900.63 18.5466 282 282 326.163 335.936 326 337 8.16522 9.6867 0 0 0 0 0.342323 8.40734e-005 0 0 0 0 0 0 0 0 0 21921.4 123.127 243.352 2.44371 0.332649 1 1 9.61008e-066 3.91256e-055 1 1 1 1 0 363.006 342.791 8.16522 9.6867 0 108126 453.102 1200.32 8.99277 0.332649 1
15 -0.00330575 0.0683113 0.961403 0 0 1 1 324.783 322.32 10.9057 7.2065 0 0 0 2 61 61 420.475 435.148 419 435 15.3857 16.0248 270 270 323.419 332.511 324 332 7.48225 10.0791 0 0 0 0 0.418958 0.000132955 0 0 0 0 0 0 0 0 0 60.2135 95.7811 2.02188 2.1415 0.3911 1 1 3.4401e-040 8.57384e-054 1 1 1 1 0 360.262 339.366 7.48225 10.0791 1 324.783 322.32 10.9057 7.2065 0.3911 1
16 -0.313806 0.0964319 0.00113726 0 0 1 1 270.464 131.312 9.62326 5.74 0 2 0 2 56 56 406.929 376.679 406.5 378 12.8994 11.9729 287 287 320.153 330.638 320 331 7.28665 10.3641 0 0 0 0 0.00726533 0.000352641 0 0 0 0 0 0 0 0 0 49.9319 39.1857 1.77661 1.71291 0.00661476 1 1 5.4462e-037 9.58265e-035 1 1 1 1 0 356.997 337.493 7.28665 10.3641 0 270.464 131.312 9.62326 5.74 0.00661476 1
17 -0.050897 0.112436 0.650782 0 0 1 1 161.008 143.202 7.3548 6.17284 1 0 0 0 59 59 390.322 383.61 390 385 9.80753 13.6218 287 287 323.906 333.801 324 333 7.47267 9.01624 0 0 0 0 -0.00601315 0.000253989 0 0 0 0 0 0 0 0 0 29.5727 42.9535 1.35088 1.85154 -0.00541986 1 1 1.14653e-033 3.00132e-034 1 1 1 1 0 360.749 340.657 7.47267 9.01624 1 161.008 143.202 7.3548 6.17284 -0.00541986 1
18 0.534727 0.073336 3.06593e-013 0 0 1 1 207.048 709.249 9.95557 12.9022 0 1 0 0 59 59 398.864 550.661 396 550 13.8483 29.1788 283 283 323.65 332.961 324 332 6.59313 8.91659 0 0 0 0 0.356808 0.000181418 0 0 0 0 0 0 0 0 0 38.3709 210.845 1.845 3.83555 0.345325 1 1 4.59327e-030 3.29298e-053 1 1 1 1 0 360.494 339.816 6.59313 8.91659 0 207.048 709.249 9.95557 12.9022 0.345325 1
19 0.460652 0.0950976 1.27259e-006 0 0 1 1 116.45 336.348 8.11961 8.19707 0 3 1 0 56 56 381.661 443.018 382.5 443 10.8398 17.7912 280 280 323.3 335.879 323 336 6.53987 9.47849 0 0 0 0 0.181046 0.000216871 0 0 0 0 0 0 0 0 0 21.5173 100.284 1.50033 2.444 0.170049 1 1 1.51105e-021 2.4868e-046 1 1 1 1 0 360.143 342.734 6.53987 9.47849 0 116.45 336.348 8.11961 8.19707 0.170049 1
20 0.016149 0.361539 0.964372 42.0761 0 1 1 42.0761 43.6701 6.68402 4.44099 3 0 2 0 56 56 364.161 354.643 363.5 355 7.42178 10.744 280 280 323.671 332.764 323 332.5 6.73826 8.73965 0 0 0 0 -0.0387136 7.3104e-005 0 0 0 0 0 0 0 0 0 3.64592 15.0233 1.07041 1.52778 -0.0336991 1 1 0.00106673 7.67491e-015 1 1 0 0 0 360.515 339.62 6.73826 8.73965 1 22.7664 43.6701 6.68402 4.44099 -0.0336991 1

Total number of rows: 21446

Table truncated, full table size 8017 Kbytes.




Supplementary data files not provided

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