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Sample GSM14678 Query DataSets for GSM14678
Status Public on Jan 09, 2004
Title 2-cell embryo replication 4
Sample type RNA
 
Channel 1
Source name 2-cell embryo
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name Universal Control
Organism Mus musculus
Extracted molecule total RNA
 
 
Description 2-cell embryo replication 4
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(r) background (selected by user)
rPValFeatEqBG P-value from t-test of significance between r Mean signal and g(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 59.0015 52.7235 -2 0.16019 8.99823e-036 0 0 1 1 106479 125.572 866.594 6.23503 0 1 0 0 75 75 16303.8 448.88 16462 448 1114.55 13.4415 228 228 394.833 403.539 394 403 7.68822 8.84538 0 0 0 0 -0.035724 0.958852 0 0 0 0 1 0 0 1 0 15819 36.8877 128.746 1.83158 -0.0163617 1 1 2.12154e-087 2.53091e-042 157 157 1 1 0 484.715 411.992 44.044 12.185 0 106479 125.572 866.594 6.23503 -0.0163617 1
2 80.8788 54.2292 -2 0.160197 9.0569e-036 0 0 1 1 68222.1 82.4338 1625.82 6.02464 0 1 7 0 65 65 11025.3 435.277 11598 435 2025.02 11.259 208 208 394.231 401.822 395 402 7.07275 8.3082 0 0 0 0 -0.154103 0.958852 1 0 0 0 0 0 0 0 0 10540.6 23.2846 251.197 1.70175 -0.118782 1 1 2.69584e-048 7.2655e-027 157 157 1 0 0 484.715 411.992 44.044 12.185 0 68222.1 82.4338 1625.82 6.02464 -0.118782 1
3 101.374 53.3596 -0.024787 0.101796 0.807622 0 0 1 1 177.226 167.394 12.4546 9.90097 0 4 0 1 70 70 540.4 435.243 539.5 436 14.3894 8.13551 214 214 391.491 402.495 392 403 7.07952 8.52213 0 0 0 0 -0.161783 0.958852 0 0 0 0 0 0 0 0 0 55.6849 23.2505 3.91329 1.37522 0.558774 1 1 1.05119e-032 7.91938e-040 157 157 0 0 0 484.715 411.992 44.044 12.185 0 177.226 167.394 12.4546 9.90097 0.558774 1
4 123.281 53.801 -0.0757649 0.0762429 0.320354 0 0 1 1 288.321 242.165 12.4799 11.9023 0 0 0 0 76 76 575.868 445.421 574 446 15.6225 11.545 221 221 392.303 403.597 392 404 6.94154 8.46843 0 0 0 0 0.0550901 0.958852 0 0 0 0 0 0 0 1 0 91.1534 33.4287 3.94553 1.64301 0.525782 1 1 2.0295e-060 9.84827e-046 157 157 0 1 0 484.715 411.992 44.044 12.185 0 288.321 242.165 12.4799 11.9023 0.525782 1
5 144.185 53.7094 -2 0.1602 9.08225e-036 0 0 1 1 118823 147.354 1070.58 5.95463 0 0 0 0 76 76 17973.8 455.684 17706.5 456.5 1373.36 12.847 207 207 397.783 403.014 398 402 8.06323 8.2111 0 0 0 0 -0.247289 0.958852 0 0 0 0 0 0 0 0 0 17489 43.6919 157.574 1.7656 -0.194566 1 1 5.2148e-085 2.77163e-053 157 157 1 1 0 484.715 411.992 44.044 12.185 0 118823 147.354 1070.58 5.95463 -0.194566 1
6 165.685 54.727 -2 0.160227 9.32216e-036 0 0 1 1 81377.1 113.776 933.703 6.66629 0 0 13 0 62 62 12750.4 444.935 12890.5 444.5 1107.79 13.1285 201 201 398.458 405.776 398 406 7.54649 8.76953 0 0 0 0 0.145971 0.958852 0 0 0 0 0 0 0 1 0 12265.7 32.9432 140.733 1.93019 0.138118 1 1 8.59242e-066 4.96495e-032 157 157 1 1 0 484.715 411.992 44.044 12.185 0 81377.1 113.776 933.703 6.66629 0.138118 1
7 187.277 53.1419 0.0341742 0.0752336 0.649656 0 0 1 1 259.294 280.521 13.2061 13.3076 1 2 0 0 73 73 566.699 450.712 568 451 19.2554 13.314 216 216 398.171 405.31 398 405 7.83987 8.84077 0 0 0 0 0.237977 0.958852 0 0 0 0 0 0 0 1 0 81.9836 38.72 4.17551 1.83684 0.536318 1 1 7.33272e-051 9.39296e-044 157 157 0 1 0 484.715 411.992 44.044 12.185 0 259.294 280.521 13.2061 13.3076 0.536318 1
8 208.25 54.4666 0.0280407 0.0639883 0.66123 0 0 1 1 363.075 387.291 13.2046 13.6122 1 0 0 0 75 75 594.52 467.88 594 468 16.413 14.7803 217 217 399.069 405.286 399 405 8.24901 9.2512 0 0 0 0 0.109777 0.958852 0 0 0 0 0 0 0 1 0 109.805 55.8877 3.99346 1.9643 0.463103 1 1 3.30433e-073 4.1057e-056 157 157 0 1 0 484.715 411.992 44.044 12.185 0 363.075 387.291 13.2046 13.6122 0.463103 1
9 229.58 53.3687 -2 0.160238 9.42561e-036 0 0 1 1 119793 176.842 1063.47 6.36597 0 1 0 0 75 75 18001.1 464.773 17915 466 1346.35 14.136 206 206 397.83 404.529 398 404 8.44929 9.39053 0 0 0 0 -0.251486 0.958852 0 0 0 0 0 0 0 1 0 17516.4 52.781 155.503 1.90001 -0.204901 1 1 1.38177e-084 4.30103e-056 157 157 1 1 0 484.715 411.992 44.044 12.185 0 119793 176.842 1063.47 6.36597 -0.204901 1
10 250.361 54.6801 -2 0.160187 8.97035e-036 0 0 1 1 80531.6 92.8653 843.406 5.9588 0 0 13 1 61 61 12748.1 438.607 12492 438 1002.73 10.964 208 208 397.308 404.76 397 404 7.94495 8.63595 0 0 0 0 -0.124995 0.958852 0 0 0 0 0 0 0 1 0 12263.4 26.6142 128.434 1.70773 -0.0877662 1 1 2.49189e-067 1.10593e-030 157 157 1 0 0 484.715 411.992 44.044 12.185 0 80531.6 92.8653 843.406 5.9588 -0.0877662 1
11 272.351 53.3541 -0.0924439 0.0794573 0.244651 0 0 1 1 274.604 221.954 12.4834 11.4665 0 1 1 0 73 73 571.534 442.63 570 442 15.3343 10.6699 219 219 397.146 402.863 397 403 7.53381 9.31751 0 0 0 0 0.206821 0.958852 0 0 0 0 0 0 0 0 0 86.8192 30.6378 3.94677 1.5828 0.598888 1 1 4.56e-057 1.2197e-043 157 157 0 0 0 484.715 411.992 44.044 12.185 0 274.604 221.954 12.4834 11.4665 0.598888 1
12 292.646 54.2008 -0.173506 0.077149 0.024514 0 0 1 1 320.514 214.952 12.6513 13.2698 1 1 0 0 74 74 586.054 441.662 585 442.5 16.4224 13.3522 214 214 395.051 400.556 394.5 401 8.60572 7.65967 0 0 0 0 -0.137417 0.958852 0 0 0 0 0 0 0 0 0 101.339 29.6699 4.00005 1.83164 0.391785 1 1 3.04753e-067 3.55456e-033 157 157 0 0 0 484.715 411.992 44.044 12.185 0 320.514 214.952 12.6513 13.2698 0.391785 1
13 313.732 54.3862 -2 0.160159 8.7216e-036 0 0 1 1 117172 115.089 1067.97 5.39974 0 1 0 0 74 74 17887 445.811 17928 446 1364.12 10.7852 209 209 396.086 401.684 396 402 7.49245 8.49184 0 0 0 0 0.0670742 0.958852 0 0 0 0 0 0 0 0 0 17402.3 33.8185 158.615 1.58669 0.0660103 1 1 7.61997e-083 1.276e-048 157 157 1 1 0 484.715 411.992 44.044 12.185 0 117172 115.089 1067.97 5.39974 0.0660103 1
14 335.306 54.94 -2 0.160137 8.53872e-036 0 0 1 1 86882.9 73.1238 1034.71 5.3623 0 1 11 1 63 63 13824.2 432.778 13706 432 1260.63 9.31604 219 219 395.973 400.452 396 401 7.51385 7.07309 0 0 0 0 0.176691 0.958852 0 0 0 0 0 0 0 0 0 13339.4 20.7855 158.863 1.52424 0.14956 1 1 1.28044e-065 5.72098e-028 157 157 1 0 0 484.715 411.992 44.044 12.185 0 86882.9 73.1238 1034.71 5.3623 0.14956 1
15 356.489 54.2362 -0.163716 0.0904122 0.0701761 0 0 1 1 245.911 168.679 12.3455 12.4113 0 3 0 0 73 73 562.288 435.329 562 434 14.3231 12.0912 202 202 394.817 400.208 396 400 5.73122 7.77458 0 0 0 0 0.18366 0.958852 0 0 0 0 0 0 0 0 0 77.5726 23.3365 3.89438 1.71709 0.555314 1 1 2.12569e-050 1.92195e-027 157 157 0 0 0 484.715 411.992 44.044 12.185 0 245.911 168.679 12.3455 12.4113 0.555314 1
16 377.52 54.751 -0.196422 0.0775877 0.011354 0 0 1 1 327.38 208.271 11.9738 11.0798 2 5 2 2 65 65 588.231 440.738 588 442 11.3396 9.51525 213 213 392.624 400.291 392 400 7.59405 7.98346 0 0 0 0 0.12554 0.958852 0 0 0 0 0 0 0 0 0 103.516 28.7462 3.78605 1.52926 0.602101 1 1 4.43859e-069 1.84373e-041 157 157 0 0 0 484.715 411.992 44.044 12.185 0 327.38 208.271 11.9738 11.0798 0.602101 1
17 398.222 54.5352 -2 0.160156 8.6959e-036 0 0 1 1 122192 117.797 1055.73 5.13398 0 4 0 2 70 70 18591.3 446.686 18412 446.5 1308.53 9.6872 206 206 393.791 400.345 393 400 8.23142 8.0233 0 0 0 0 -0.0901849 0.958852 0 0 0 0 0 0 0 0 0 18106.6 34.6934 156.439 1.51205 -0.0551845 1 1 7.93312e-081 3.88073e-053 157 157 1 1 0 484.715 411.992 44.044 12.185 0 122192 117.797 1055.73 5.13398 -0.0551845 1
18 420.229 55.3358 -2 0.160141 8.57278e-036 0 0 1 1 86370.6 74.8661 987.553 6.16388 0 0 10 0 65 65 13733.5 433.292 13631 435 1220.98 11.7656 221 221 395.186 400.796 394 401 7.99301 8.98176 0 0 0 0 0.242527 0.958852 0 0 0 0 0 0 0 0 0 13248.8 21.3 151.485 1.75367 0.214105 1 1 2.22941e-068 8.09572e-023 157 157 1 0 0 484.715 411.992 44.044 12.185 0 86370.6 74.8661 987.553 6.16388 0.214105 1
19 440.49 54.4877 -0.122506 0.0887287 0.167376 0 0 1 1 240.284 181.225 12.5654 10.6361 1 0 0 0 75 75 560.547 437.053 561 437 15.8969 9.55623 197 197 395.975 400.599 395 400 8.40095 7.16045 0 0 0 0 0.211074 0.958852 0 0 0 0 0 0 0 0 0 75.8316 25.061 3.96552 1.47082 0.63526 1 1 1.50314e-048 1.64033e-039 157 157 0 0 0 484.715 411.992 44.044 12.185 0 240.284 181.225 12.5654 10.6361 0.63526 1
20 462.234 55.0168 -0.157993 0.0743788 0.0336563 0 0 1 1 335.27 233.025 12.513 12.5139 2 3 0 0 70 70 590.671 444.171 591 444.5 15.1578 11.9516 224 224 395.366 399.817 396 399 7.87514 8.20245 0 0 0 0 0.117755 0.958852 0 0 0 0 0 0 0 0 0 105.956 32.1791 3.95451 1.72808 0.524226 1 1 1.56264e-070 4.15407e-039 157 157 0 1 0 484.715 411.992 44.044 12.185 0 335.27 233.025 12.513 12.5139 0.524226 1

Total number of rows: 22575

Table truncated, full table size 8753 Kbytes.




Supplementary data files not provided
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