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Sample GSM47152 Query DataSets for GSM47152
Status Public on Apr 21, 2005
Title D-4-3
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 04, 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 40.7218 33.3111 -1.32829 0.111746 1.38888e-032 0 0 1 1 9339.86 438.585 159.582 9.75904 0 0 0 0 62 62 1766.87 422.726 1721.5 422.5 185.478 16.1196 280 280 282.186 311.457 282 312 4.18666 6.32158 0 0 0 0 0.0660261 -1.34321e-005 0 0 0 0 0 0 0 0 0 1378.73 93.5571 23.557 2.08176 0.0649261 1 1 2.58199e-055 8.65166e-051 1 1 1 1 0 388.146 329.169 4.18666 6.32158 0 9339.86 438.585 159.582 9.75904 0.0649261 1
2 61.7978 33.565 0 0.153613 1 24.3424 37.2095 1 1 24.3424 37.2095 7.75473 7.10134 1 2 1 0 55 55 358.018 332.818 358 332 10.1297 8.79202 284 284 282.074 310.412 282 310 4.36394 6.53579 0 0 0 0 0.112737 7.03855e-005 0 0 0 0 1 0 0 0 0 -30.0157 4.69467 1.39022 1.24734 0.105278 0 1 2.16809e-029 0.000358208 1 1 0 0 0 388.034 328.124 4.36394 6.53579 0 -167.43 26.7276 7.75473 7.10134 0.105278 0
3 83 33.3807 0.347262 0.0560993 6.0115e-010 0 0 1 1 1082.7 2408.64 21.2958 22.1543 0 2 4 2 54 54 550.685 832.463 554.5 832.5 23.4527 33.9771 278 278 281.968 310.205 282 310 4.16913 6.62435 0 0 0 0 0.348726 -0.000379998 0 0 0 0 0 0 0 0 0 162.758 504.546 3.20129 4.64073 0.346382 1 1 4.52777e-047 1.00269e-064 1 1 1 1 0 387.928 327.917 4.16913 6.62435 0 1082.7 2408.64 21.2958 22.1543 0.346382 1
4 103.911 33.1895 0.308978 0.0625667 7.87727e-007 0 0 1 1 335.045 682.466 9.23051 12.1452 5 1 0 0 57 57 444.86 454.702 444 454 11.635 16.865 273 273 282.227 309.941 282 309 4.14086 5.77172 0 0 0 0 0.0650328 -0.00015178 0 0 0 0 0 0 0 0 0 56.6726 127.049 1.56134 2.26097 0.063415 1 1 4.71567e-042 8.81943e-053 1 1 1 1 0 388.187 327.653 4.14086 5.77172 0 335.045 682.466 9.23051 12.1452 0.063415 1
5 125.036 33.5751 -0.0336348 0.0492171 0.494356 0 0 1 1 11112.8 10284.6 97.1105 83.1936 0 0 0 0 60 60 1855.97 2781.27 1852 2751 99.289 153.666 277 277 282.859 310.563 282 310 4.40171 7.00986 0 0 0 0 0.78741 2.54197e-005 0 0 0 0 0 0 0 0 0 1467.15 2452.99 12.8209 19.8426 0.787065 1 1 4.95514e-071 5.24319e-073 1 1 1 1 0 388.819 328.275 4.40171 7.00986 1 11112.8 10284.6 97.1105 83.1936 0.787065 1
6 146.082 33.0442 0.387269 0.0568516 9.63028e-012 0 0 1 1 2765.82 6746.73 98.5334 53.2475 0 3 0 3 56 56 775.964 1844.55 731 1843 103.234 89.5585 271 271 282.705 309.683 282 310 4.27325 6.33413 0 0 0 0 0.0723854 6.14045e-005 1 0 0 0 0 0 0 0 0 387.3 1517.16 13.7977 11.9739 0.0723353 1 1 2.68801e-034 1.20188e-069 1 1 1 1 0 388.665 327.394 4.27325 6.33413 0 2765.82 6746.73 98.5334 53.2475 0.0723353 1
7 167.906 33.8288 -1.34164 0.112679 1.09176e-032 0 0 1 1 9949.58 453.067 141.265 9.9593 1 1 0 0 61 61 1852.36 425.934 1823 425 162.267 16.3594 278 278 282.968 311.227 283 311 4.47726 6.64378 0 0 0 0 0.328886 1.39873e-005 0 0 0 0 0 0 0 0 0 1463.43 96.9963 20.7779 2.13217 0.323065 1 1 2.09011e-059 1.11489e-050 1 1 1 1 0 388.928 328.938 4.47726 6.64378 0 9949.58 453.067 141.265 9.9593 0.323065 1
8 188.962 33.3562 0.0559914 0.0664703 0.399591 0 0 1 1 322.705 367.11 13.4188 10.7414 0 0 0 0 61 61 445.525 394.295 447 392 18.1976 14.7573 278 278 283.065 310.558 282 311 5.02802 6.71078 0 0 0 0 0.185911 0.000398319 0 0 0 0 0 0 0 0 0 56.4999 66.026 2.3494 1.93187 0.180338 1 1 3.83316e-033 1.70886e-043 1 1 1 1 0 389.025 328.269 5.02802 6.71078 1 322.705 367.11 13.4188 10.7414 0.180338 1
9 209.992 33.9114 0.802552 0.224877 0.000358558 25.1239 0 1 1 25.1239 159.455 6.97135 8.92732 0 0 1 0 60 60 376.283 357.3 375 357.5 9.45837 11.8068 286 286 283.643 311.58 284 311 4.50404 6.22549 0 0 0 0 0.0049934 -0.000194177 0 0 0 0 0 0 0 0 0 -13.3199 28.008 1.24978 1.56807 0.00473264 0 1 7.02206e-016 5.57232e-027 1 1 0 1 0 389.603 329.292 4.50404 6.22549 0 -74.2996 159.455 6.97135 8.92732 0.00473264 1
10 230.934 33.3208 1.1481 0.156023 1.85995e-013 25.789 0 1 1 25.789 362.686 7.89533 10.609 2 1 0 0 57 57 394.175 391.982 396 391 10.8794 13.2591 287 287 284.655 312.871 285 313 4.79687 6.37034 0 0 0 0 0.228171 0.000170732 0 0 0 0 0 0 0 0 0 3.56046 61.3998 1.46857 1.79601 0.218934 0 1 0.0183409 1.34764e-041 1 1 0 1 0 390.615 330.583 4.79687 6.37034 0 19.1418 362.686 7.89533 10.609 0.218934 1
11 252.174 34.0529 0.347943 0.0674905 2.53046e-007 0 0 1 1 259.402 577.984 11.4482 12.5048 0 0 1 1 61 61 436.508 437.246 435 436 15.2868 17.4763 279 279 285.663 314.351 285 314 5.09772 6.92134 0 0 0 0 -0.107653 0.000107803 0 0 0 0 0 0 0 0 0 44.8852 105.183 1.98093 2.27566 -0.104587 1 1 5.71367e-032 5.57536e-051 1 1 1 1 0 391.623 332.063 5.09772 6.92134 0 259.402 577.984 11.4482 12.5048 -0.104587 1
12 274.025 33.653 0.422604 0.078922 8.56963e-008 0 0 1 1 169.928 449.645 8.46572 10.8776 4 0 1 0 56 56 421.625 411.464 422 409.5 11.0529 14.022 282 282 285.34 314.411 285 315 5.33281 6.98608 0 0 0 0 0.020618 0.000399198 0 0 0 0 0 0 0 0 0 30.3246 79.3414 1.51076 1.9194 0.0196964 1 1 2.36721e-028 4.51895e-046 1 1 1 1 0 391.3 332.123 5.33281 6.98608 0 169.928 449.645 8.46572 10.8776 0.0196964 1
13 294.988 33.6135 0.166359 0.0513195 0.00118844 0 0 1 1 1488.72 2183.6 15.4714 21.1598 2 0 4 0 55 55 612.327 793.927 613 790 16.9608 33.0302 285 285 284.593 314.649 285 314 4.82394 6.94265 0 0 0 0 -0.101901 -0.000126054 0 0 0 0 0 0 0 0 0 221.774 461.567 2.30478 4.47274 -0.100688 1 1 1.29447e-063 1.40886e-064 1 1 1 1 0 390.553 332.361 4.82394 6.94265 0 1488.72 2183.6 15.4714 21.1598 -0.100688 1
14 316 33.5187 -1.36936 0.114645 6.94238e-033 0 0 1 1 10449.4 446.402 145.353 8.42899 4 1 0 0 55 55 1926.6 428.2 1905 427 158.332 13.0304 290 290 285.662 314.797 285 315 5.39347 7.17671 0 0 0 0 0.0798623 0.000505866 0 0 0 0 0 0 0 0 0 1534.98 95.6919 21.3518 1.80686 0.0776529 1 1 2.57052e-055 2.65375e-052 1 1 1 1 0 391.622 332.508 5.39347 7.17671 0 10449.4 446.402 145.353 8.42899 0.0776529 1
15 336.589 33.9645 -0.577494 0.0672481 8.88666e-018 0 0 1 1 1602.73 424.001 23.6351 10.7324 1 3 0 0 56 56 645.464 414.107 644 410 28.1864 15.5302 285 285 283.418 312.835 283 312 4.60989 6.89388 0 0 0 0 0.08362 0.000212118 0 0 0 0 0 0 0 0 0 256.087 83.5605 3.77645 2.11511 0.0818349 1 1 3.91687e-055 2.61499e-044 1 1 1 1 0 389.377 330.547 4.60989 6.89388 0 1602.73 424.001 23.6351 10.7324 0.0818349 1
16 357.988 33.4783 0.586351 0.0723252 5.18263e-016 0 0 1 1 235.107 907.018 15.0585 15.2313 0 1 0 1 58 58 429.034 497.155 427.5 494 19.3771 21.3145 282 282 283.16 311.213 283 311 4.18769 6.45963 0 0 0 0 0.227115 0.000151815 0 0 0 0 0 0 0 0 0 39.915 168.231 2.55653 2.82504 0.223929 1 1 1.87769e-022 1.63365e-054 1 1 1 1 0 389.119 328.924 4.18769 6.45963 0 235.107 907.018 15.0585 15.2313 0.223929 1
17 379.228 34.16 0.167751 0.05075 0.000948293 0 0 1 1 3788.43 5574.55 31.8048 34.2821 0 2 0 0 61 61 917.066 1589.64 918 1585 34.575 60.391 273 273 282.868 313 283 313 4.3476 6.44205 0 0 0 0 0.359276 -0.000215413 0 0 0 0 0 0 0 0 0 528.238 1258.93 4.43469 7.74209 0.358187 1 1 2.13722e-073 2.08601e-081 1 1 1 1 0 388.828 330.712 4.3476 6.44205 0 3788.43 5574.55 31.8048 34.2821 0.358187 1
18 400.518 33.5183 0.0715575 0.0500576 0.152859 0 0 1 1 1762.59 2078.3 23.7079 24.3197 0 2 0 0 58 58 650 771.672 648.5 768.5 26.6958 39.2126 268 268 282.716 312.552 283 313 4.25694 6.72863 0 0 0 0 0.409816 -1.02604e-005 0 0 0 0 0 0 0 0 0 261.324 441.409 3.51496 5.16524 0.407397 1 1 6.10417e-059 1.76485e-062 1 1 1 1 0 388.676 330.264 4.25694 6.72863 1 1762.59 2078.3 23.7079 24.3197 0.407397 1
19 421.985 34.1818 -0.166678 0.0506579 0.00100093 0 0 1 1 9737.8 6634.12 119.95 93.3126 1 0 0 0 63 63 1697.37 1886.21 1678 1834 127.929 173.52 273 273 282.799 313.978 283 314 4.11057 6.61712 0 0 0 0 0.868504 0.000258342 0 0 0 0 0 0 0 0 0 1308.61 1554.52 16.1194 21.8651 0.868255 1 1 1.081e-064 3.64085e-061 1 1 1 1 0 388.758 331.69 4.11057 6.61712 1 9737.8 6634.12 119.95 93.3126 0.868255 1
20 442.917 33.6632 -0.0252313 0.0493404 0.60909 0 0 1 1 3850.78 3633.44 66.6564 49.6118 0 0 0 0 60 60 933.933 1141.05 918 1130 73.0423 85.4471 284 284 282.986 314.912 283 315 4.58525 6.75487 0 0 0 0 0.638562 -0.000449657 0 0 0 0 0 0 0 0 0 544.987 808.426 9.43365 11.0384 0.637875 1 1 1.06517e-053 9.49885e-060 1 1 1 1 0 388.946 332.624 4.58525 6.75487 1 3850.78 3633.44 66.6564 49.6118 0.637875 1

Total number of rows: 22493

Table truncated, full table size 8745 Kbytes.




Supplementary data files not provided

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