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Sample GSM14720 Query DataSets for GSM14720
Status Public on Jan 09, 2004
Title 43h-AC replication 2
Sample type RNA
 
Channel 1
Source name 43h-AC, early 2-cell embryo
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name Universal Reference
Organism Mus musculus
Extracted molecule total RNA
 
 
Description 43h-AC replication 2
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 94.1886 72.3566 -2 0.160055 7.87661e-036 0 0 1 1 532899 181.662 5324.82 11.6184 0 0 0 0 76 76 12961.3 412.632 12743 412 1094.36 11.1341 206 206 368.451 388.578 368 388 3.96387 7.29927 0 0 0 0 0.297913 0.274911 0 0 0 0 0 0 0 1 0 12563.1 20.0694 125.532 1.28356 0.296482 1 1 1.35474e-081 1.55735e-025 151 151 1 1 0 398.222 392.562 2.94144 1.57175 0 532899 181.662 5324.82 11.6184 0.296482 1
2 115.115 70.6504 -2 0.160037 7.73959e-036 0 0 1 1 442135 101.306 5134.63 8.57651 0 0 0 1 74 74 9901.3 404.838 9676 405 949.364 8.87204 222 222 367.486 387.41 367 388 4.565 7.05111 0 0 0 0 -0.0740479 0.274911 0 0 0 0 0 0 0 0 0 9503.08 12.2757 110.362 1.03925 -0.0734114 1 1 3.69772e-075 8.22921e-019 151 151 1 1 0 398.222 392.562 2.94144 1.57175 0 442135 101.306 5134.63 8.57651 -0.0734114 1
3 136.292 72.2333 0 0.269715 1 26.0878 68.0436 1 1 26.0878 68.0436 7.19933 41.3486 0 2 0 0 74 74 396.027 394.757 397 396 6.67232 8.14225 215 215 366.405 387.563 366 388 4.02202 7.04024 0 0 0 0 0.176627 0.274911 0 0 0 0 0 0 0 0 0 -2.19489 2.19459 0.811737 0.95512 0.178109 0 0 0.0082382 0.0243426 151 151 0 0 0 398.222 392.562 2.94144 1.57175 0 -19.4665 95.0072 7.19933 41.3486 0.178109 0
4 157.623 71.3525 -0.773502 0.272298 0.00450222 0 23.4778 1 1 139.367 23.4778 20.8911 14.5278 1 1 0 0 73 73 403.644 394.315 404 395 6.63612 8.23758 226 226 366.659 386.912 366.5 387 4.1584 7.63158 0 0 0 0 0.0584849 0.274911 0 0 0 0 0 0 0 0 0 5.42192 1.7529 0.812748 0.972583 0.0660536 1 0 2.34653e-009 0.0755376 151 151 0 0 0 398.222 392.562 2.94144 1.57175 0 139.367 26.1837 20.8911 14.5278 0.0660536 0
5 179.579 72.7554 -2 0.160051 7.85102e-036 0 0 1 1 562284 180.062 5764.31 12.2329 2 0 0 0 73 73 13720.1 412.356 13412 411 1166.85 11.4375 218 218 366.945 386.5 366 386 3.95093 7.62318 0 0 0 0 0.10651 0.274911 0 0 0 0 0 0 0 0 0 13321.8 19.794 136.57 1.34475 0.106072 1 1 3.13375e-078 1.37423e-023 151 151 1 1 0 398.222 392.562 2.94144 1.57175 0 562284 180.062 5764.31 12.2329 0.106072 1
6 200.211 71.5222 -2 0.160029 7.68464e-036 0 0 1 1 462783 85.0853 5459.61 8.16696 0 1 0 0 75 75 10185.9 403.04 9997 402 999.989 8.63907 217 217 366.24 386.078 366 386 4.02512 7.36787 0 0 0 0 -0.00430444 0.274911 0 0 0 0 0 0 0 0 0 9787.7 10.4778 115.469 1.00572 -0.004197 1 1 1.89031e-075 2.52142e-016 151 151 1 1 0 398.222 392.562 2.94144 1.57175 0 462783 85.0853 5459.61 8.16696 -0.004197 1
7 221.453 72.5214 -1.215 0.265676 4.80289e-006 0 21.2215 1 1 348.154 21.2215 25.5195 13.0763 4 1 0 0 71 71 410.465 394.282 411 395 7.28762 8.08912 206 206 366.646 385.354 366.5 385 4.17959 7.06179 0 0 0 0 0.115279 0.274911 0 0 0 0 0 0 0 0 0 12.2429 1.71953 0.897396 0.968485 0.119814 1 0 1.10651e-022 0.0800155 151 151 1 0 0 398.222 392.562 2.94144 1.57175 0 348.154 23.2167 25.5195 13.0763 0.119814 0
8 242.252 71.7479 -0.988973 0.261242 0.000153305 0 21.6774 1 1 211.339 21.6774 20.1008 12.9023 0 0 0 0 75 75 405.813 394.907 407 396 5.89937 8.02559 217 217 368.24 385.184 368 385 4.1952 7.67832 0 0 0 0 0.000483313 0.274911 0 0 0 0 0 0 0 0 0 7.59142 2.3445 0.722033 0.935501 0.0129129 1 0 1.74985e-017 0.0143193 151 151 0 0 0 398.222 392.562 2.94144 1.57175 0 211.339 32.335 20.1008 12.9023 0.0129129 0
9 263.65 72.6447 -2 0.160047 7.82121e-036 0 0 1 1 572201 169.397 5230.98 9.56591 0 1 0 1 73 73 13889.7 411.274 13770 411 1053.79 8.96174 220 220 367.455 384.65 367 384.5 4.46424 7.95939 0 0 0 0 -0.0456428 0.274911 0 0 0 0 0 0 0 0 0 13491.5 18.7118 123.337 1.05666 -0.0452425 1 1 8.6533e-082 2.3692e-028 151 151 1 1 0 398.222 392.562 2.94144 1.57175 0 572201 169.397 5230.98 9.56591 -0.0452425 1
10 284.29 72.0214 -2 0.160025 7.6512e-036 0 0 1 1 476819 74.4532 5711.29 9.04906 1 1 0 0 74 74 10351.8 401.851 10065 400.5 1025.59 9.64959 221 221 365.774 384.67 366 385 4.16625 8.00707 0 0 0 0 0.0641675 0.274911 0 0 0 0 0 0 0 0 0 9953.58 9.28919 119.223 1.12901 0.0638168 1 1 3.45541e-074 4.43507e-012 151 151 1 1 0 398.222 392.562 2.94144 1.57175 0 476819 74.4532 5711.29 9.04906 0.0638168 1
11 305.847 72.6186 0 0.308435 1 26.0878 68.0436 1 1 26.0878 68.0436 7.96141 46.7039 1 0 1 0 73 73 397.329 393.616 397 393 7.39192 9.15246 228 228 366.298 384.548 366 384 3.90736 7.79599 0 0 0 0 0.140257 0.274911 0 0 0 0 0 0 0 0 0 -0.893145 1.05427 0.897662 1.07882 0.142916 0 0 0.322636 0.33163 151 151 0 0 0 398.222 392.562 2.94144 1.57175 0 -7.92134 45.6411 7.96141 46.7039 0.142916 0
12 327.069 71.9008 -0.493389 0.221801 0.0261173 0 0 1 1 120.497 38.6889 22.5546 14.3727 1 3 0 1 64 64 402.766 395.234 403 395 6.52892 7.8755 218 218 366.381 384.72 366 385 3.9533 7.53974 0 0 0 0 -0.147709 0.274911 0 0 0 0 0 0 0 0 0 4.54371 2.67221 0.850495 0.992713 -0.130588 1 1 9.71044e-007 0.00902214 151 151 0 0 0 398.222 392.562 2.94144 1.57175 0 120.497 38.6889 22.5546 14.3727 -0.130588 1
13 347.468 73.4565 -2 0.160052 7.85948e-036 0 0 1 1 559109 182.87 4965.8 13.0228 6 0 0 0 70 70 13659.4 412.643 13481.5 414 985.423 11.9164 205 205 366.795 385.663 367 386 4.31561 7.87207 0 0 0 0 0.0103877 0.274911 0 0 0 0 0 0 0 0 0 13261.2 20.0807 117.781 1.43002 0.0103961 1 1 6.11706e-080 4.63817e-022 151 151 1 1 0 398.222 392.562 2.94144 1.57175 0 559109 182.87 4965.8 13.0228 0.0103961 1
14 369.723 71.9144 -2 0.160037 7.74068e-036 0 0 1 1 463205 106.568 4998 9.17724 0 0 0 0 75 75 10475.5 405.32 10270 403 941.665 9.44995 226 226 365.827 385.655 366 386 4.40115 7.48542 0 0 0 0 -0.01007 0.274911 0 0 0 0 0 0 0 0 0 10077.3 12.7578 108.734 1.09866 -0.00993109 1 1 2.71983e-078 1.62598e-018 151 151 1 1 0 398.222 392.562 2.94144 1.57175 0 463205 106.568 4998 9.17724 -0.00993109 1
15 390.048 73.8871 0 0.251606 1 26.0878 68.0436 1 1 26.0878 68.0436 7.58322 34.8867 0 3 0 0 66 66 398.47 391.606 399 392 6.66846 6.46381 213 213 366.141 386.324 366 387 3.95122 7.35445 0 0 0 0 0.0286294 0.274911 0 0 0 0 0 0 0 0 0 0.247785 -0.956103 0.855021 0.805856 0.0393521 0 0 0.772756 0.239553 151 151 0 0 1 398.222 392.562 2.94144 1.57175 0 2.19762 -41.3911 7.58322 34.8867 0.0393521 0
16 411.678 72.6777 -0.636218 0.16525 0.000118099 0 0 1 1 194.201 44.8779 22.0631 12.6702 0 2 0 0 73 73 404.986 395.918 404 396 6.23942 8.02038 223 223 366.314 386.314 366 386 3.84616 7.93669 0 0 0 0 -0.0752366 0.274911 0 0 0 0 0 0 0 0 0 6.76439 3.35564 0.768499 0.947389 -0.0592784 1 1 1.06535e-013 0.00068832 151 151 0 0 0 398.222 392.562 2.94144 1.57175 0 194.201 44.8779 22.0631 12.6702 -0.0592784 1
17 432.577 74.3063 -2 0.160057 7.89593e-036 0 0 1 1 567429 202.296 4761.67 11.7477 3 2 1 0 69 69 14030.6 414.493 13863 414 950.257 10.5254 214 214 366.71 387.981 367 388 4.34435 7.54017 0 0 0 0 0.0818769 0.274911 0 0 0 0 0 0 0 0 0 13632.3 21.9306 114.398 1.27354 0.0815205 1 1 1.09881e-080 9.35455e-027 151 151 1 1 0 398.222 392.562 2.94144 1.57175 0 567429 202.296 4761.67 11.7477 0.0815205 1
18 453.947 72.0938 -2 0.160049 7.83119e-036 0 0 1 1 449290 136.57 3970.85 9.48871 0 1 0 1 67 67 10439.4 408.478 10236 409 726.401 8.9905 242 242 367.26 387.021 367 387 4.68271 7.16518 0 0 0 0 -0.113037 0.274911 0 0 0 0 0 0 0 0 0 10041.2 15.9154 88.7443 1.10579 -0.112192 1 1 2.63946e-077 2.70635e-022 151 151 1 1 0 398.222 392.562 2.94144 1.57175 0 449290 136.57 3970.85 9.48871 -0.112192 1
19 475.222 74.2906 0 0.218791 1 49.6345 35.7635 1 1 49.6345 35.7635 12.5221 19.1731 0 2 1 0 73 73 399.384 392.877 399 393 6.00146 7.11599 218 218 366.876 388.564 367 389 4.26736 7.56952 0 0 0 0 0.36992 0.274911 0 0 0 0 0 0 0 1 0 1.16165 0.314548 0.742084 0.842629 0.35955 0 0 0.121036 0.709977 151 151 0 0 0 398.222 392.562 2.94144 1.57175 0 19.6019 7.1572 12.5221 19.1731 0.35955 0
20 496.265 73.2045 -0.406171 0.122541 0.000917798 0 0 1 1 218.396 85.7185 24.2904 14.063 2 0 1 0 72 72 405.139 399.611 406 399 6.20383 9.75265 213 213 367.427 387.493 368 388 3.89976 6.7318 0 0 0 0 -0.03378 0.274911 0 0 0 0 0 0 0 0 0 6.91698 7.04895 0.769316 1.15646 -0.0224455 1 1 4.87266e-014 4.74862e-008 151 151 0 1 0 398.222 392.562 2.94144 1.57175 0 218.396 85.7185 24.2904 14.063 -0.0224455 1

Total number of rows: 22575

Table truncated, full table size 8854 Kbytes.




Supplementary data files not provided
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