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Sample GSM47064 Query DataSets for GSM47064
Status Public on Apr 21, 2005
Title D-2-1
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 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 23.0742 33.0386 -1.21633 0.103929 1.2232e-031 0 0 1 1 8624.41 524.085 111.793 29.074 0 1 0 0 60 60 1329.02 81.3833 1308.5 79.5 123.526 10.2115 259 259 38.4324 52.7645 38 53 3.59024 6.63168 0 0 0 0 0.133679 0.000594209 0 0 0 0 0 0 0 0 0 1230.39 24.8973 15.9487 1.3812 0.127581 1 1 5.76278e-061 3.41044e-028 1 1 1 1 0 98.6314 56.486 3.59024 6.63168 0 8624.41 524.085 111.793 29.074 0.127581 1
2 43.5 33 0 0.109909 1 60.7576 47.0142 1 1 60.7576 47.0142 13.9349 8.49906 0 1 2 0 57 57 97.9825 58.1404 97 58 5.35688 7.79294 284 284 38.588 53.3486 39 53 3.20269 6.04474 0 0 0 0 0.28067 5.70615e-005 0 0 0 0 0 0 0 0 0 -0.804505 1.07025 0.734546 1.09275 0.256096 0 0 0.277499 0.330743 1 1 0 0 1 98.787 57.0701 3.20269 6.04474 0 -15.2621 8.32407 13.9349 8.49906 0.256096 0
3 65.1771 33.7069 -0.243414 0.0530416 4.45154e-006 0 0 1 1 2212.22 1263.04 17.6428 34.4819 0 1 0 0 61 61 411.311 116.459 412 115 19.4238 12.6235 279 279 38.2043 52.2186 38 52 3.44189 5.72501 0 0 0 0 -0.119341 5.79303e-005 0 0 0 0 0 0 0 0 0 312.908 60.5189 2.49549 1.65221 -0.116345 1 1 3.87737e-075 2.4026e-045 1 1 1 1 0 98.4032 55.9401 3.44189 5.72501 0 2212.22 1263.04 17.6428 34.4819 -0.116345 1
4 86.301 32.9955 -0.00220596 0.0605785 0.970951 0 0 1 1 434.443 432.242 18.0677 37.3437 0 0 0 0 61 61 159.066 78 161 78 19.4712 13.9344 290 290 38.7241 53.1172 39 53 3.44303 6.79864 0 0 0 0 0.407453 -0.000146609 0 0 0 0 0 0 0 0 0 60.1425 21.1612 2.50122 1.82824 0.396316 1 1 9.46082e-033 1.49672e-017 1 1 1 1 0 98.9231 56.8388 3.44303 6.79864 1 434.443 432.242 18.0677 37.3437 0.396316 1
5 107.852 33.2363 -0.420356 0.0581545 4.89224e-013 0 0 1 1 5845.31 2220.5 48.6374 48.946 2 0 0 0 60 60 948.817 159.8 946.5 159.5 54.7365 17.4121 277 277 39.0542 52.5343 39 52 3.17268 6.58086 0 0 0 0 0.335449 -0.000237442 0 0 0 0 0 0 0 0 0 849.564 103.544 7.06902 2.2824 0.330256 1 1 2.56264e-072 1.1731e-049 1 1 1 1 0 99.2531 56.2558 3.17268 6.58086 0 5845.31 2220.5 48.6374 48.946 0.330256 1
6 128.916 32.656 -0.572113 0.0647808 1.0327e-018 0 0 1 1 9572.32 2563.92 94.6797 58.1496 0 0 0 0 60 60 1518.15 173.2 1507 173 108.733 20.3718 282 282 38.6028 52.2872 39 53 3.31905 6.45095 0 0 0 0 0.306582 -3.40847e-005 0 0 0 0 0 0 0 0 0 1419.35 117.191 14.0388 2.6579 0.303332 1 1 7.58912e-068 2.85197e-048 1 1 1 1 0 98.8018 56.0087 3.31905 6.45095 0 9572.32 2563.92 94.6797 58.1496 0.303332 1
7 148.968 33.7435 -1.49536 0.123785 1.34244e-033 0 0 1 1 9172.73 293.185 102.414 26.4865 0 0 0 0 62 62 1395.29 69.871 1356.5 70.5 113.983 9.42004 279 279 38.4086 52.0932 38 52 3.69007 7.11154 0 0 0 0 0.176715 0.000230116 0 0 0 0 0 0 0 0 0 1296.68 14.0563 14.4776 1.26985 0.166468 1 1 1.80601e-066 1.34157e-017 1 1 1 0 0 98.6075 55.8147 3.69007 7.11154 0 9172.73 293.185 102.414 26.4865 0.166468 1
8 170.123 32.8246 -0.117997 0.0532236 0.026622 0 0 1 1 945.134 720.271 11.8279 30.5751 0 0 0 0 63 63 229.905 90.6825 230 92 12.9611 11.3519 287 287 38.1185 51.899 38 52 3.60554 6.98001 0 0 0 0 0.0116304 0.000292601 0 0 0 0 0 0 0 0 0 131.587 35.0621 1.64676 1.48837 0.0110926 1 1 6.28137e-066 9.78555e-036 1 1 1 1 0 98.3174 55.6205 3.60554 6.98001 0 945.134 720.271 11.8279 30.5751 0.0110926 1
9 192.881 33.1116 0.230994 0.139993 0.0989352 0 0 1 1 89.4772 152.302 7.84287 18.8759 1 2 1 1 57 57 110.281 62.807 110 63 7.91191 6.49846 287 287 37.892 51.5087 38 51 3.52893 6.35976 0 0 0 0 0.251832 -7.50362e-005 0 0 0 0 0 0 1 0 0 12.1898 7.57679 1.06846 0.939045 0.226397 1 1 1.02305e-016 6.52226e-012 1 1 1 0 0 98.0909 55.2302 3.52893 6.35976 1 89.4772 152.302 7.84287 18.8759 0.226397 1
10 213.66 33.092 -0.0772476 0.0630208 0.220294 0 0 1 1 429.117 359.193 10.7213 26.7939 1 0 0 0 59 59 158.034 73.7627 156 74 11.2709 9.65319 278 278 38.464 52.446 38 52 3.6236 6.31104 0 0 0 0 -0.165841 3.37647e-005 0 0 0 0 0 0 0 0 0 59.3709 17.5952 1.48335 1.3125 -0.15708 1 1 2.83864e-045 7.11907e-021 1 1 1 1 0 98.663 56.1676 3.6236 6.31104 0 429.117 359.193 10.7213 26.7939 -0.15708 1
11 233.913 33.2835 0.109515 0.0546129 0.0449319 0 0 1 1 601.139 773.553 12.8793 34.0941 2 0 0 0 59 59 181.831 93.7288 182 91 13.6674 12.3872 273 273 38.1319 52.2637 38 52 3.06141 6.74455 0 0 0 0 0.0067507 0.000128165 0 0 0 0 0 0 0 0 0 83.4997 37.7436 1.78897 1.66353 0.00651237 1 1 1.94657e-048 9.08064e-033 1 1 1 1 0 98.3308 55.9852 3.06141 6.74455 0 601.139 773.553 12.8793 34.0941 0.00651237 1
12 255.185 33.0915 0.0431233 0.0651438 0.507989 0 0 1 1 342.386 378.128 11.4082 25.1188 0 1 0 0 62 62 145.694 74.2903 146.5 73 12.3389 9.22112 272 272 38.1287 52.0441 38 52 3.09177 6.23449 0 0 0 0 0.214468 0.000269879 0 0 0 0 0 0 0 0 0 47.3659 18.5247 1.57822 1.23058 0.202663 1 1 6.24174e-039 2.9734e-024 1 1 1 1 0 98.3276 55.7656 3.09177 6.23449 1 342.386 378.128 11.4082 25.1188 0.202663 1
13 275.831 33.9076 -0.209704 0.0519157 5.36045e-005 0 0 1 1 2856.64 1762.59 19.7578 42.0271 2 0 1 0 60 60 507.233 140.683 507.5 141.5 21.813 15.1417 273 273 38.7143 53.3883 39 53 3.52497 6.39417 0 0 0 0 0.239465 -0.000170113 0 0 0 0 0 0 0 0 0 408.32 83.5735 2.82412 1.99272 0.234232 1 1 1.12745e-077 4.14411e-048 1 1 1 1 0 98.9132 57.1098 3.52497 6.39417 0 2856.64 1762.59 19.7578 42.0271 0.234232 1
14 297.452 33.6983 -1.58215 0.130157 5.35351e-034 0 0 1 1 9541.6 249.731 109.954 33.5982 1 1 0 0 57 57 1445.56 68.9649 1428 70 117.149 11.8427 279 279 38.7348 53.2509 39 53 3.45181 6.3093 0 0 0 0 0.248213 0.000291008 0 0 0 0 0 0 0 0 0 1346.63 11.9925 15.5181 1.61344 0.241294 1 1 2.08349e-061 3.61419e-010 1 1 1 0 0 98.9337 56.9724 3.45181 6.3093 0 9541.6 249.731 109.954 33.5982 0.241294 1
15 319.174 33.9246 0.445234 0.0603521 1.61557e-013 0 0 1 1 695.647 1939.2 11.7113 46.4215 0 1 0 0 62 62 196.145 150.194 197 150 12.8265 17.411 276 276 38.4928 52.6558 38 52 3.24457 6.52556 0 0 0 0 0.257458 0.000400007 0 0 0 0 0 0 0 0 0 97.4535 93.8162 1.64064 2.24581 0.251695 1 1 7.09701e-057 1.25851e-048 1 1 1 1 0 98.6917 56.3773 3.24457 6.52556 0 695.647 1939.2 11.7113 46.4215 0.251695 1
16 340.063 33.2194 -0.405491 0.0631648 1.36664e-010 0 0 1 1 898.468 353.193 12.8579 25.515 0 0 1 0 62 62 223 73.4355 223 73 13.9613 9.31528 274 274 38.1533 52.4599 38 52 3.23531 6.49713 0 0 0 0 0.132858 -9.68698e-005 0 0 0 0 0 0 0 0 0 124.648 17.2541 1.78383 1.24645 0.125337 1 1 4.90529e-061 2.40297e-022 1 1 1 1 0 98.3522 56.1814 3.23531 6.49713 0 898.468 353.193 12.8579 25.515 0.125337 1
17 360.935 34.0705 -0.0912445 0.0497562 0.0666791 0 0 1 1 4125.44 3343.69 31.8189 56.1836 0 0 0 0 63 63 698.81 212.095 705 215 36.7168 20.544 282 282 38.1702 52.6738 38 52 3.69275 6.40006 0 0 0 0 0.0326969 1.31673e-005 0 0 0 0 0 0 0 0 0 600.44 155.7 4.63111 2.61621 0.0323117 1 1 1.75831e-077 3.17769e-058 1 1 1 1 0 98.3691 56.3953 3.69275 6.40006 1 4125.44 3343.69 31.8189 56.1836 0.0323117 1
18 382.16 32.9213 -0.245167 0.0532545 4.15077e-006 0 0 1 1 2007.13 1141.32 22.7898 37.0936 0 1 0 0 62 62 381.645 110.339 382.5 109 25.2626 13.753 283 283 38.3216 51.7809 38 52 3.40199 5.96039 0 0 0 0 0.243018 1.10839e-005 0 0 0 0 0 0 0 0 0 283.125 54.8363 3.21472 1.78221 0.237696 1 1 2.06423e-066 6.7549e-041 1 1 1 1 0 98.5205 55.5024 3.40199 5.96039 0 2007.13 1141.32 22.7898 37.0936 0.237696 1
19 403.256 33.5638 0.0587049 0.0493612 0.234324 0 0 1 1 7251.58 8301.14 88.3622 112.049 0 0 0 0 58 58 1227.86 417.138 1208.5 418 104.787 37.0137 283 283 38.3887 52.1449 38 52 3.15174 6.70848 0 0 0 0 0.599157 4.68561e-005 0 0 0 0 0 0 0 0 0 1129.27 361.272 13.7605 4.87647 0.597095 1 1 6.87136e-061 5.79436e-059 1 1 1 1 0 98.5876 55.8664 3.15174 6.70848 1 7251.58 8301.14 88.3622 112.049 0.597095 1
20 424.13 32.939 0.119219 0.0499923 0.0170907 0 0 1 1 4414 5808.33 24.2561 74.88 0 1 1 0 62 62 754.823 321.645 754 317.5 28.3292 26.711 284 284 38.8732 52.9472 39 53 3.42173 6.77404 0 0 0 0 0.0463205 -0.000246332 0 0 0 0 0 0 0 0 0 655.75 264.976 3.60353 3.41604 0.045924 1 1 1.33832e-085 5.08449e-064 1 1 1 1 0 99.0722 56.6687 3.42173 6.77404 1 4414 5808.33 24.2561 74.88 0.045924 1

Total number of rows: 22493

Table truncated, full table size 8713 Kbytes.




Supplementary data files not provided
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