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Sample GSM14718 Query DataSets for GSM14718
Status Public on Jan 09, 2004
Title 32h-AC replication 3
Sample type RNA
 
Channel 1
Source name 32h-AC, late 1-cell embryo
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name Universal Reference
Organism Mus musculus
Extracted molecule total RNA
 
 
Description 32h-AC replication 3
Keywords = preimplantation
Keywords = development
 
Submission date Dec 30, 2003
Last update date May 28, 2005
Contact name Minoru S.H. Ko
E-mail(s) [email protected]
Phone 410-558-8359
Organization name NIH
Department National Institute on Aging
Lab Lab of Genetics
Street address 251 Bayview Blvd, Suite 100, 10C
City Baltimore
State/province MD
ZIP/Postal code 21224
Country USA
 
Platform ID GPL870
Series (1)
GSE936 Dynamics of global gene expression changes during mouse preimplantation development

Data table header descriptions
ID_REF Feature number
PositionX Found X coordinate of feature centroid in pixels
PositionY Found Y coordinate of feature centroid in pixels
VALUE 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. A feature is considered found if the found spot centroid is within the bounds of the spot deviation limit with respect to corresponding nominal centroid.
rIsFound A boolean used to flag found (strong) features.The flag is applied independently in each channel. A feature is considered found if the found spot centroid is within the bounds of the spot deviation limit with respect to corresponding nominal centroid.
gProcessedSignal Dye-normalized signal after surrogate algorithm, green channel, used for computation of log ratio
rProcessedSignal Dye-normalized signal after surrogate algorithm, red channel, used for computation of log ratio
gProcessedSigError Standard error of propagated feature signal, green channel
rProcessedSigError Standard error of propagated feature signal, red channel
gNumPixOLHi Number of outlier pixels per feature with intensity > upper threshold set via the pixel outlier rejection method. The number is computed independently in each channel. These pixels are omitted from all subsequent calculations.
rNumPixOLHi Number of outlier pixels per feature with intensity > upper threshold set via the pixel outlier rejection method. The number is computed independently in each channel. These pixels are omitted from all subsequent calculations.
gNumPixOLLo Number of outlier pixels per feature with intensity < lower threshold set via the pixel outlier rejection method. The number is computed independently in each channel. NOTE: The pixel outlier method is the ONLY step that removes data in Feature Extraction.
rNumPixOLLo Number of outlier pixels per feature with intensity < lower threshold set via the pixel outlier rejection method. The number is computed independently in each channel. NOTE: The pixel outlier method is the ONLY step that removes data in Feature Extraction.
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 Raw median signal of feature in green channel (inlier pixels)
rMedianSignal Raw median signal of feature in red 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
rIsSaturated Boolean flag indicating if a feature is saturated or not
PixCorrelation Ratio of estimated feature covariance in RedGreen space to product of feature Standard Deviation in Red Green space.
BGPixCorrelation Ratio of estimated background covariance in RedGreen space to product of background Standard Deviation in Red Green space.
gIsFeatNonUnifOL Boolean flag indicating if a feature is NonUniformity Outlier or not Green Channel
rIsFeatNonUnifOL Boolean flag indicating if a feature is NonUniformity Outlier or not Red Channel
gIsBGNonUnifOL Boolean flag indicating if background is NonUniformity Outlier or not Green Channel
rIsBGNonUnifOL Boolean flag indicating if background is NonUniformity Outlier or not Red Channel
gIsFeatPopnOL Boolean flag indicating if a feature is a Population Outlier or not for Green Channel. 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 for Red Channe. Probes with replicate features on a microarray are examined using population statistics
gIsBGPopnOL Boolean flag indicating if background is a Population Outlier or not for Green Channel.
rIsBGPopnOL Boolean flag indicating if background is a Population Outlier or not for Red Channel.
IsManualFlag Manual Flag
gBGSubSignal The net g signal following the subtraction of the background from the raw mean g signal
rBGSubSignal The net r signal following the subtraction of the background from the raw mean r signal
gBGSubSigError Propagated standard error as computed on net g background subtracted signal
rBGSubSigError Propagated standard error as computed on net r background subtracted signal
BGSubSigCorrelation Ratio of estimated background subtracted feature signal covariance in RG space to product of background subtracted feature Standard Deviation in RG space
gIsPosAndSignif Boolean flag indicating 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 indicating 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 Mean signal and g background (selected by user)
rPValFeatEqBG P-value from t-test of significance between r Mean signal and r background (selected by user)
gNumBGUsed Number of local background regions or features used to calculate the background subtraction on this feature g channel.
rNumBGUsed Number of local background regions or features used to calculate the background subtraction on this feature r channel.
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 A boolean used to flag features used for computation of global BG offset
gBGUsed Background value (after global background adjust if turned ON) subtracted from the raw mean signal to generate the BG subtracted signal; this value is computed per channel. If global BG subtraction is used the column is identical for every feature in a given channel
rBGUsed Background value (after global background adjust if turned ON) subtracted from the raw mean signal to generate the BG subtracted signal; this value is computed per channel. If global BG subtraction is used the column is identical for every feature in a given channel
gBGSDUsed Standard deviation of background used in g channel
rBGSDUsed Standard deviation of background used in r channel
IsNormalization A 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 81.0173 69.1035 -1.58668 0.130435 4.80015e-034 0 0 1 1 12501.5 323.801 132.52 16.6183 0 0 0 0 69 69 2814.17 432.261 2784 432 208.846 14.2175 224 224 375.071 391.929 375 391 5.01069 8.3082 0 0 0 0 0.283997 0.544803 0 0 0 0 0 0 0 0 0 2372.05 33.5497 25.1444 1.72185 0.283401 1 1 7.5743e-074 6.62724e-030 300 152 1 1 0 442.126 398.711 5.85793 2.31474 0 12501.5 323.801 132.52 16.6183 0.283401 1
2 102.545 68.4889 -1.61509 0.132681 4.33998e-034 0 0 1 1 7635.32 185.24 107.475 11.7519 2 0 0 0 74 74 1843.42 418.554 1807 419 169.652 10.708 221 221 375.937 392.145 376 391 5.42767 8.67163 0 0 0 0 0.0553245 0.544803 0 0 0 0 0 0 0 0 0 1401.29 19.8428 19.7245 1.25886 0.056655 1 1 3.6628e-069 1.028e-025 300 152 1 1 0 442.126 398.711 5.85793 2.31474 0 7635.32 185.24 107.475 11.7519 0.056655 1
3 123.145 69.5 0 0.212474 1 69.8276 9.87757 1 1 69.8276 9.87757 12.8605 4.57272 5 4 0 0 67 67 440.358 399.612 440 400 8.38596 8.63565 214 214 375.107 389.692 375 390 4.50275 8.021 0 0 0 0 0.0107359 0.544803 0 0 0 0 0 0 0 0 0 -1.76776 0.900724 1.07889 1.07159 0.0520748 0 0 0.105198 0.403453 300 152 0 0 1 442.126 398.711 5.85793 2.31474 0 -21.072 3.84361 12.8605 4.57272 0.0520748 0
4 144.529 69.816 0 0.112038 1 69.8276 0 1 1 69.8276 23.9096 11.2548 4.90336 2 4 0 0 70 70 436.457 404.314 437 404.5 7.37541 9.48461 207 207 375.763 388.647 376 388 4.46421 7.40416 0 0 0 0 -0.0242518 0.544803 0 0 0 0 0 0 0 0 0 -5.66883 5.60307 0.944182 1.14907 0.022458 0 1 3.95423e-008 6.15903e-006 300 152 0 0 0 442.126 398.711 5.85793 2.31474 0 -67.5734 23.9096 11.2548 4.90336 0.022458 0
5 165.886 69.7287 -1.58558 0.130352 4.84261e-034 0 0 1 1 12607.5 327.38 149.617 17.2445 2 0 0 0 73 73 2836.33 432.603 2819 431 242.741 15.1683 217 217 375.806 389.636 376 389 5.40485 7.3498 0 0 0 0 0.296987 0.544803 0 0 0 0 0 0 0 0 0 2394.2 33.8915 28.4127 1.78521 0.296277 1 1 1.04078e-073 4.40539e-030 300 152 1 1 0 442.126 398.711 5.85793 2.31474 0 12607.5 327.38 149.617 17.2445 0.296277 1
6 186.588 69.0877 -1.71317 0.140015 2.00701e-034 0 0 1 1 7690.72 148.868 101.95 11.0687 2 1 0 0 72 72 1847.92 414.722 1807 415 158.1 9.97493 221 221 376.095 389.186 376 389 4.95204 7.69752 0 0 0 0 0.086428 0.544803 0 0 0 0 0 0 0 0 0 1405.79 16.011 18.6354 1.19046 0.087523 1 1 1.45479e-069 1.22951e-021 300 152 1 1 0 442.126 398.711 5.85793 2.31474 0 7690.72 148.868 101.95 11.0687 0.087523 1
7 206.945 70.2698 0 0.174056 1 69.8276 9.87757 1 1 69.8276 9.87757 13.24 3.64893 1 1 0 2 71 71 438.986 400.958 438 401 8.91466 7.0294 213 213 375.357 387.028 375 387 5.16286 7.44408 0 0 0 0 0.0355538 0.544803 0 0 0 0 0 0 0 1 0 -3.14006 2.24653 1.11072 0.855103 0.0842097 0 0 0.00585871 0.0103803 300 152 0 0 0 442.126 398.711 5.85793 2.31474 0 -37.43 9.58648 13.24 3.64893 0.0842097 0
8 228.7 70.0032 0 0.127391 1 69.8276 0 1 1 69.8276 21.1087 14.173 4.91896 0 0 0 0 76 76 438.158 403.658 438 406 9.93721 9.91504 217 217 375.249 387.7 376 388 4.47243 8.25394 0 0 0 0 0.0682183 0.544803 0 0 0 0 0 0 0 0 0 -3.96808 4.94668 1.18899 1.15273 0.099987 0 1 0.00123777 4.98702e-005 300 152 0 0 0 442.126 398.711 5.85793 2.31474 0 -47.3002 21.1087 14.173 4.91896 0.099987 0
9 250.297 69.7972 -1.60731 0.131957 3.94596e-034 0 0 1 1 13045 322.207 158.401 14.0932 1 0 0 0 75 75 2921.43 432.04 2867 430 260.703 12.5196 225 225 376.96 387.111 377 387 5.52294 8.1865 0 0 0 0 0.000665426 0.544803 0 0 0 0 0 0 0 0 0 2479.3 33.3288 30.1053 1.45779 0.00176725 1 1 1.5142e-074 6.21949e-036 300 152 1 1 0 442.126 398.711 5.85793 2.31474 0 13045 322.207 158.401 14.0932 0.00176725 1
10 271.189 70.0865 -1.76493 0.143915 1.41873e-034 0 0 1 1 7790.05 133.848 93.1668 11.4037 3 0 0 0 69 69 1863.74 413.13 1826 412 141.202 10.0848 219 219 377.758 388.712 377 388 5.94939 8.11185 0 0 0 0 0.149769 0.544803 0 0 0 0 0 0 0 0 0 1421.61 14.4192 17.0021 1.2285 0.150307 1 1 2.45848e-070 2.56252e-018 300 152 1 1 0 442.126 398.711 5.85793 2.31474 0 7790.05 133.848 93.1668 11.4037 0.150307 1
11 292.891 70.0938 0 0.243857 1 83.5725 8.25304 1 1 83.5725 8.25304 17.0742 4.10487 1 1 0 0 69 69 442.13 399.13 441 398 9.53617 9.4354 222 222 377.149 389.203 377 390 6.46679 8.52515 0 0 0 0 -0.173274 0.544803 0 0 0 0 0 0 0 0 0 0.00446286 0.419219 1.1968 1.1513 -0.128714 0 0 0.997034 0.716835 300 152 0 0 1 442.126 398.711 5.85793 2.31474 0 0.0636696 1.49469 17.0742 4.10487 -0.128714 0
12 313.26 70.5271 0 0.10934 1 69.8276 0 1 1 69.8276 24.5868 12.5771 4.68262 0 2 0 0 74 74 441.878 404.473 443 403.5 8.59747 9.3005 214 214 376.35 388.967 376 389 6.49258 7.65843 0 0 0 0 0.0382477 0.544803 0 0 0 0 0 0 0 0 0 -0.247594 5.76176 1.05511 1.09734 0.0776716 0 1 0.815002 1.29147e-006 300 152 0 0 0 442.126 398.711 5.85793 2.31474 0 -2.95136 24.5868 12.5771 4.68262 0.0776716 0
13 334.903 70.6091 -1.54844 0.127603 6.90531e-034 0 0 1 1 13241.1 374.523 165.961 14.7024 0 1 0 0 75 75 2977.77 437.16 2933 437 275.219 12.9699 225 225 374.858 387.231 375 387 4.50568 7.55574 0 0 0 0 0.324803 0.544803 0 0 0 0 0 0 0 0 0 2535.65 38.4488 31.7814 1.50935 0.323275 1 1 1.54753e-073 4.61297e-039 300 152 1 1 0 442.126 398.711 5.85793 2.31474 0 13241.1 374.523 165.961 14.7024 0.323275 1
14 355.976 70.3186 -1.54214 0.12726 8.47734e-034 0 0 1 1 8047.54 230.952 114.038 12.2927 1 0 0 0 75 75 1927.72 423.307 1894 423 182.29 11.2201 239 239 375.18 389.824 375 390 5.09624 8.58096 0 0 0 0 0.0073037 0.544803 0 0 0 0 0 0 0 0 0 1485.59 24.5955 21.0517 1.30912 0.00899077 1 1 1.17288e-069 1.64668e-030 300 152 1 1 0 442.126 398.711 5.85793 2.31474 0 8047.54 230.952 114.038 12.2927 0.00899077 1
15 377.128 71.1278 0 0.218514 1 69.8276 9.87757 1 1 69.8276 9.87757 13.536 4.79643 0 0 0 1 72 72 439.111 401.097 439 401 9.19822 9.40356 218 218 375.257 390.101 375 390 4.87144 7.77381 0 0 0 0 0.0736372 0.544803 0 0 0 0 0 0 0 0 0 -3.01486 2.38601 1.13555 1.12401 0.107385 0 0 0.00946235 0.0370697 300 152 0 0 0 442.126 398.711 5.85793 2.31474 0 -35.9377 10.1817 13.536 4.79643 0.107385 0
16 398.386 71.1607 0 0.0875121 1 69.8276 0 1 1 69.8276 42.8525 13.0076 6.10126 2 0 0 0 73 73 438.603 408.753 438 410 8.86432 12.1104 225 225 375.351 390.276 375 390 4.59778 7.88786 0 0 0 0 0.254341 0.544803 0 0 0 0 0 0 0 0 0 -3.52323 10.0422 1.09122 1.42979 0.270872 0 1 0.00174917 8.61261e-010 300 152 0 1 0 442.126 398.711 5.85793 2.31474 0 -41.9975 42.8525 13.0076 6.10126 0.270872 0
17 419.375 70.9289 -1.49861 0.123951 1.18823e-033 0 0 1 1 12940.5 410.526 152.081 16.5254 0 1 0 0 75 75 2928.24 440.72 2861 440 253.015 14.5542 218 218 375.45 390.784 375 390 5.09538 7.23435 0 0 0 0 0.238073 0.544803 0 0 0 0 0 0 0 0 0 2486.11 42.0088 29.2176 1.69103 0.237569 1 1 1.37967e-075 3.52534e-038 300 152 1 1 0 442.126 398.711 5.85793 2.31474 0 12940.5 410.526 152.081 16.5254 0.237569 1
18 440.544 70.9199 -1.56945 0.12928 6.48811e-034 0 0 1 1 7938.15 213.93 102.848 12.6645 3 0 0 0 72 72 1904.46 421.542 1860 422 160.738 11.3571 230 230 376.452 391.309 377 391 4.88603 8.12702 0 0 0 0 0.0124535 0.544803 0 0 0 0 0 0 0 0 0 1462.33 22.8305 18.9462 1.35155 0.0142287 1 1 2.92439e-070 4.52432e-027 300 152 1 1 0 442.126 398.711 5.85793 2.31474 0 7938.15 213.93 102.848 12.6645 0.0142287 1
19 462.067 72.0667 0 0.154653 1 69.8276 0 1 1 69.8276 14.3478 10.9429 4.81023 0 1 0 0 68 68 437.412 402.074 437 401.5 7.03771 9.16567 221 221 375.24 390.204 375 390 4.75791 7.82822 0 0 0 0 0.0541298 0.544803 0 0 0 0 0 0 0 0 0 -4.71421 3.36231 0.918019 1.12725 0.0965845 0 1 1.64008e-006 0.00391522 300 152 0 0 0 442.126 398.711 5.85793 2.31474 0 -56.1942 14.3478 10.9429 4.81023 0.0965845 0
20 482.887 71.8225 0 0.0977748 1 69.8276 0 1 1 69.8276 42.3359 12.9268 5.53254 1 3 0 0 68 68 439.456 408.632 440 408 8.49659 10.5786 221 221 373.932 390.81 374 390 4.51562 7.52391 0 0 0 0 -0.0221854 0.544803 0 0 0 0 0 0 0 0 0 -2.67009 9.92114 1.08445 1.29651 0.0137099 0 1 0.0159057 8.05049e-011 300 152 0 1 0 442.126 398.711 5.85793 2.31474 0 -31.8279 42.3359 12.9268 5.53254 0.0137099 0

Total number of rows: 22575

Table truncated, full table size 8793 Kbytes.




Supplementary data files not provided
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