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Sample GSM14679 Query DataSets for GSM14679
Status Public on Jan 09, 2004
Title 4-cell embryo replication 1
Sample type RNA
 
Channel 1
Source name 4-cell embryo
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name Universal Control
Organism Mus musculus
Extracted molecule total RNA
 
 
Description 4-cell embryo replication 1
Keywords = preimplantation
Keywords = development
 
Submission date Dec 30, 2003
Last update date May 28, 2005
Contact name Minoru S.H. Ko
E-mail(s) kom@mail.nih.gov
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 63.4157 60.8825 -2 0.160241 9.45642e-036 0 0 1 1 96184.8 143.628 547.675 7.49408 0 2 0 0 73 73 13629.1 426.836 13560 428 640.012 9.57139 223 223 396.538 403.749 396 403 8.12332 8.68983 0 0 0 0 -0.109181 0.810766 0 0 0 0 0 0 0 1 0 13158 22.9638 74.9216 1.19818 -0.0965403 1 1 1.35294e-096 4.08574e-034 154 154 1 1 0 471.067 403.872 17.8435 5.27509 0 96184.8 143.628 547.675 7.49408 -0.0965403 1
2 85.0282 59.7225 -2 0.160294 9.9537e-036 0 0 1 1 57813.9 104.1 509.976 7.20498 0 1 3 0 72 72 8427.31 420.417 8324 418 595.389 9.02227 216 216 396.231 403.315 395.5 403 7.74249 8.46514 0 0 0 0 0.0646753 0.810766 0 0 0 0 0 0 0 1 0 7956.24 16.5448 70.1819 1.14511 0.0662076 1 1 4.87239e-082 1.19571e-025 154 154 1 1 0 471.067 403.872 17.8435 5.27509 0 57813.9 104.1 509.976 7.20498 0.0662076 1
3 105.791 61.4242 0.265297 0.143374 0.0642576 83.5751 0 1 1 83.5751 153.948 9.73982 11.8107 4 2 0 1 70 70 480.643 419.643 480 419.5 12.5687 9.47772 226 226 394.982 401.823 394 401 7.38284 8.85009 0 0 0 0 0.192844 0.810766 0 0 0 0 0 0 0 1 0 9.57563 15.771 2.07947 1.20993 0.327389 1 1 7.68845e-006 2.38812e-022 154 154 0 1 0 471.067 403.872 17.8435 5.27509 0 44.8503 153.948 9.73982 11.8107 0.327389 1
4 127.163 60.5528 0.0867029 0.113604 0.445343 0 0 1 1 135.699 165.683 9.17096 11.277 0 0 0 0 76 76 501.961 419.789 502 419.5 13.1974 8.68764 215 215 393.702 399.088 393 398 7.59087 7.65596 0 0 0 0 -0.145554 0.810766 0 0 0 0 0 0 0 0 0 30.8933 15.9176 2.08787 1.08341 0.121998 1 1 1.1762e-033 4.93067e-027 154 154 0 1 0 471.067 403.872 17.8435 5.27509 0 135.699 165.683 9.17096 11.277 0.121998 1
5 147.809 61.6638 -2 0.160206 9.13448e-036 0 0 1 1 103764 132.241 706.852 9.90489 0 4 6 0 71 71 14666.6 425.014 14663 425 814.731 12.8536 216 216 393.662 399.389 393 399 7.35237 8.40745 0 0 0 0 -0.113641 0.810766 0 0 0 0 0 0 0 1 0 14195.6 21.1422 96.7015 1.58356 -0.106222 1 1 6.38773e-089 3.5968e-022 154 154 1 1 0 471.067 403.872 17.8435 5.27509 0 103764 132.241 706.852 9.90489 -0.106222 1
6 169.366 60.252 -2 0.160173 8.84601e-036 0 0 1 1 60172 63.3304 437.178 8.35715 1 1 6 0 68 68 8809.37 413.868 8758 414.5 499.429 10.2969 225 225 394.231 397.471 394 397 7.65961 7.9922 0 0 0 0 -0.0985527 0.810766 0 0 0 0 0 0 0 0 0 8338.3 9.9958 60.5817 1.31906 -0.0870675 1 1 5.47428e-084 4.49167e-011 154 154 1 0 0 471.067 403.872 17.8435 5.27509 0 60172 63.3304 437.178 8.35715 -0.0870675 1
7 189.722 61.3645 0 0.068557 1 87.3173 0 1 1 87.3173 77.4535 9.58353 11.2542 6 1 0 0 68 68 479.926 412.162 478 413 10.9644 9.29389 222 222 392.878 397.748 393 397 7.80756 8.03665 0 0 0 0 0.0759888 0.810766 0 0 0 0 0 0 0 0 0 8.85925 8.28992 1.95841 1.20455 0.258338 1 1 1.04829e-005 8.79185e-010 154 154 0 0 0 471.067 403.872 17.8435 5.27509 0 43.3529 77.4535 9.58353 11.2542 0.258338 0
8 211.589 60.2417 0.0805339 0.117932 0.494681 0 0 1 1 130.549 157.147 8.81625 12.6424 3 0 1 1 70 70 500.7 419.014 501 418.5 11.6449 9.55153 223 223 391.108 398.22 391 398 7.49577 8.77656 0 0 0 0 -0.0258904 0.810766 0 0 0 0 0 0 0 0 0 29.6328 15.1424 2.00117 1.2182 0.1864 1 1 9.89647e-034 3.94008e-021 154 154 0 1 0 471.067 403.872 17.8435 5.27509 0 130.549 157.147 8.81625 12.6424 0.1864 1
9 232.72 62.0677 -2 0.160176 8.87184e-036 0 0 1 1 104542 113.85 509.902 8.32945 1 1 0 0 73 73 14787.9 422.055 14787 422 596.503 10.7702 229 229 391.179 397.293 391 396 7.06041 8.45561 0 0 0 0 0.186984 0.810766 0 0 0 0 0 0 0 0 0 14316.9 18.183 69.8302 1.3303 0.182478 1 1 1.94061e-101 1.48475e-023 154 154 1 1 0 471.067 403.872 17.8435 5.27509 0 104542 113.85 509.902 8.32945 0.182478 1
10 254.413 60.4125 -2 0.16014 8.5625e-036 0 0 1 1 61302.3 51.8801 615.216 9.01031 0 0 10 0 67 67 8997.79 412.03 9037 411 700.34 11.0631 223 223 390.314 397.323 390 398 7.3448 8.69419 0 0 0 0 0.190211 0.810766 0 0 0 0 0 0 0 0 0 8526.72 8.15801 85.5722 1.41685 0.185511 1 1 1.0269e-073 1.54355e-007 154 154 1 0 0 471.067 403.872 17.8435 5.27509 0 61302.3 51.8801 615.216 9.01031 0.185511 1
11 275.208 61.5995 0 0.0643745 1 90.8585 0 1 1 90.8585 86.326 10.1675 11.0995 4 0 0 0 72 72 475.153 413.486 475 413.5 11.7565 9.84956 226 226 388.805 398.128 389 398 6.4213 8.68236 0 0 0 0 0.0696526 0.810766 0 0 0 0 0 0 0 0 0 4.08555 9.61427 1.99678 1.23617 0.246143 0 1 0.0420639 1.13167e-011 154 154 0 0 0 471.067 403.872 17.8435 5.27509 0 20.8035 86.326 10.1675 11.0995 0.246143 0
12 296.83 61.1795 0.0320991 0.1349 0.811922 0 0 1 1 117.777 126.812 9.69521 12.2582 2 1 0 0 71 71 497.451 416.254 498 416 13.7153 9.4275 226 226 388.429 397.881 388 398 6.87196 8.97992 0 0 0 0 0.255207 0.810766 0 0 0 0 0 0 0 0 0 26.3835 12.3817 2.17184 1.19687 0.369436 1 1 5.72576e-025 4.98332e-017 154 154 0 0 0 471.067 403.872 17.8435 5.27509 0 117.777 126.812 9.69521 12.2582 0.369436 1
13 318.373 62.0332 -2 0.160204 9.1208e-036 0 0 1 1 110331 139.674 586.767 7.22199 1 0 0 1 74 74 15555.6 426.216 15398 426 689.997 9.24146 223 223 387.314 396.605 387 395 6.93211 8.28416 0 0 0 0 -0.0367547 0.810766 0 0 0 0 0 0 0 0 0 15084.6 22.3444 80.2234 1.15534 -0.0288245 1 1 7.51519e-100 5.68465e-035 154 154 1 1 0 471.067 403.872 17.8435 5.27509 0 110331 139.674 586.767 7.22199 -0.0288245 1
14 339.418 61.0033 -2 0.160215 9.21397e-036 0 0 1 1 65674.7 86.4286 644.739 8.27179 0 0 8 3 65 65 9514.46 417.6 9524 416 715.677 10.0231 223 223 386.812 397.525 386 397 6.64142 8.43673 0 0 0 0 0.0651853 0.810766 0 0 0 0 0 0 0 0 0 9043.39 13.7282 88.7805 1.31388 0.0659196 1 1 1.47177e-072 1.4217e-016 154 154 1 1 0 471.067 403.872 17.8435 5.27509 0 65674.7 86.4286 644.739 8.27179 0.0659196 1
15 360.952 62.7066 0.0730417 0.166958 0.66176 88.4125 0 1 1 88.4125 104.606 9.53178 10.5334 1 2 0 1 72 72 476.375 415.208 475 414.5 10.8439 8.98972 211 211 385.431 397.863 386 396 6.66396 8.31837 0 0 0 0 0.0433985 0.810766 0 0 0 0 0 0 0 0 0 5.30778 11.3365 1.92371 1.14154 0.252416 1 1 0.00630957 2.43011e-016 154 154 0 0 0 471.067 403.872 17.8435 5.27509 0 26.2995 104.606 9.53178 10.5334 0.252416 1
16 381.66 61.6256 -0.0178242 0.125832 0.887356 0 0 1 1 135.295 129.855 10.1971 10.3643 2 3 0 2 68 68 501.603 416.456 502 416.5 14.8184 7.5041 216 216 386.796 399.81 386 399 7.06219 8.89139 0 0 0 0 0.219495 0.810766 0 0 0 0 0 0 0 1 0 30.5357 12.584 2.30145 1.00439 0.369656 1 1 3.24026e-027 5.06951e-022 154 154 0 0 0 471.067 403.872 17.8435 5.27509 0 135.295 129.855 10.1971 10.3643 0.369656 1
17 402.768 62.6753 -2 0.160171 8.83078e-036 0 0 1 1 113808 120.741 752.787 8.49681 0 2 0 0 74 74 16040.4 423.176 15812.5 422 885.819 11.099 228 228 386.066 398.338 386 398 6.85212 7.57953 0 0 0 0 0.16022 0.810766 0 0 0 0 0 0 0 0 0 15569.4 19.3038 102.984 1.35845 0.155701 1 1 6.26991e-093 1.23125e-024 154 154 1 1 0 471.067 403.872 17.8435 5.27509 0 113808 120.741 752.787 8.49681 0.155701 1
18 423.848 61.6703 -2 0.160139 8.5592e-036 0 0 1 1 68821.8 58.4437 622.224 6.87186 0 3 7 0 66 66 9997.98 413.106 10100 413 699.656 8.1167 209 209 386.254 397.971 386 397 6.47538 8.13404 0 0 0 0 0.130123 0.810766 0 0 0 0 0 0 0 0 0 9526.92 9.23422 86.1337 1.08577 0.125018 1 1 9.13332e-076 3.84758e-013 154 154 1 0 0 471.067 403.872 17.8435 5.27509 0 68821.8 58.4437 622.224 6.87186 0.125018 1
19 444.657 62.8619 0.0586902 0.173988 0.735874 85.9478 0 1 1 85.9478 98.3842 9.85622 11.4414 0 0 0 0 76 76 480.237 414.237 479.5 413 12.6921 9.8331 227 227 385.441 397.815 386 398 6.5527 8.61934 0 0 0 0 0.368446 0.810766 0 0 0 0 0 0 0 0 0 9.16962 10.365 2.04623 1.20537 0.446219 1 1 1.24918e-005 1.42318e-013 154 154 0 0 0 471.067 403.872 17.8435 5.27509 0 44.1679 98.3842 9.85622 11.4414 0.446219 1
20 466.07 62.4542 0.169453 0.13221 0.199949 0 0 1 1 102.801 151.862 8.82738 14.3224 0 0 0 0 75 75 494.147 418.667 494 417 11.8112 11.5095 214 214 385.631 396.771 385 396.5 6.12769 8.25753 0 0 0 0 -0.121707 0.810766 0 0 0 0 0 0 0 0 0 23.0794 14.7948 1.9818 1.39533 0.0994284 1 1 2.00696e-024 1.72638e-017 154 154 0 1 0 471.067 403.872 17.8435 5.27509 0 102.801 151.862 8.82738 14.3224 0.0994284 1

Total number of rows: 22575

Table truncated, full table size 8799 Kbytes.




Supplementary data files not provided
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