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Sample GSM14723 Query DataSets for GSM14723
Status Public on Jan 09, 2004
Title 32h-DMSO replication 2
Sample type RNA
 
Channel 1
Source name 32h-DMSO, 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-DMSO 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 78.2215 61.2785 -2 0.160285 9.86601e-036 0 0 1 1 156669 277.222 1394.04 15.601 0 1 0 1 73 73 14955 409.014 14653 410 1106.04 8.34581 213 213 368.244 391.779 368 391 4.31064 8.8191 0 0 0 0 0.0916767 0.631908 0 0 0 0 0 0 0 1 0 14548.6 17.73 129.453 0.997778 0.0901685 1 1 1.24628e-082 3.32918e-029 153 153 1 1 0 406.346 391.284 5.21131 2.51728 0 156669 277.222 1394.04 15.601 0.0901685 1
2 99.3931 59.6312 -2 0.160325 1.02631e-035 0 0 1 1 118912 239.908 1270.83 16.8432 3 0 0 0 72 72 11177.3 407.014 10945.5 406 976.744 9.21036 217 217 368.512 391.286 368 391 4.70334 8.19335 0 0 0 0 0.00801383 0.631908 0 0 0 0 0 0 0 1 0 10771 15.7301 115.111 1.10436 0.00830273 1 1 4.16101e-076 3.69556e-023 153 153 1 1 0 406.346 391.284 5.21131 2.51728 0 118912 239.908 1270.83 16.8432 0.00830273 1
3 120.645 61.1901 0 0.0946415 1 113.697 0 1 1 113.697 48.1328 16.3101 8.13912 2 0 0 1 73 73 405.342 397.521 405 396 5.27631 8.84136 213 213 367.099 389.869 367 390 3.99701 8.4212 0 0 0 0 -0.0419836 0.631908 0 0 0 0 0 0 0 1 0 -1.00312 6.2368 0.747572 1.05463 0.0346915 0 1 0.181817 8.48817e-008 153 153 0 0 0 406.346 391.284 5.21131 2.51728 0 -21.8855 48.1328 16.3101 8.13912 0.0346915 0
4 141.758 60.0938 0.0751258 0.162795 0.644458 0 0 1 1 90.679 107.803 13.2129 13.2838 2 6 0 0 67 67 413.194 399.761 412 400 7.40442 8.38666 223 223 367.054 389.726 367 389 4.01537 8.28173 0 0 0 0 0.110066 0.631908 0 0 0 0 0 0 0 1 0 6.84844 8.47745 0.997893 1.04461 0.149839 1 1 6.67209e-010 9.97514e-012 153 153 0 1 0 406.346 391.284 5.21131 2.51728 0 90.679 107.803 13.2129 13.2838 0.149839 1
5 163.06 61.3138 -2 0.160275 9.77106e-036 0 0 1 1 165328 282.442 1575.94 20.0892 0 0 0 0 76 76 15819.9 409.276 15642 410 1280.85 11.0147 222 222 367.95 387.793 368 388 4.13048 7.31281 0 0 0 0 -0.0222077 0.631908 0 0 0 0 0 0 0 0 0 15413.5 17.9926 146.924 1.27975 -0.0216369 1 1 4.04475e-083 3.40094e-023 153 153 1 1 0 406.346 391.284 5.21131 2.51728 0 165328 282.442 1575.94 20.0892 -0.0216369 1
6 184.601 60.3184 -2 0.160241 9.45515e-036 0 0 1 1 123725 185.161 1148.8 17.7232 3 0 0 1 70 70 11466.2 403.586 11269 403 859.178 9.70357 210 210 367.657 388.348 368 388 4.10818 7.39767 0 0 0 0 0.208708 0.631908 0 0 0 0 0 0 0 0 0 11059.8 12.302 102.692 1.17752 0.206013 1 1 1.2853e-078 3.64933e-016 153 153 1 1 0 406.346 391.284 5.21131 2.51728 0 123725 185.161 1148.8 17.7232 0.206013 1
7 205.233 61.3951 -0.346134 0.0803628 1.65377e-005 0 0 1 1 382.004 172.161 20.2995 14.723 3 3 0 0 72 72 437.028 404.014 436 404 13.3648 9.0748 201 201 367.358 386.97 367 387 3.97757 6.87671 0 0 0 0 0.1289 0.631908 0 0 0 0 1 1 0 0 0 30.6822 12.7301 1.63044 1.08867 0.152851 1 1 2.27401e-031 1.12202e-018 153 153 1 1 0 406.346 391.284 5.21131 2.51728 0 382.004 172.161 20.2995 14.723 0.152851 1
8 226.213 60.4567 0.0161819 0.213733 0.939649 72.4517 0 1 1 72.4517 75.2022 14.1253 12.501 0 2 0 0 73 73 410.068 397.493 409 399 7.89924 8.64601 215 215 366.405 385.879 366 386 3.87407 7.15739 0 0 0 0 0.13514 0.631908 0 0 0 0 0 0 0 0 0 3.72291 6.20941 1.01601 1.0322 0.172223 1 1 0.00039415 5.48469e-008 153 153 0 0 0 406.346 391.284 5.21131 2.51728 0 51.7588 75.2022 14.1253 12.501 0.172223 1
9 247.089 61.5027 -2 0.160207 9.14348e-036 0 0 1 1 168076 216.196 1462.94 16.4705 2 2 0 0 71 71 15854.7 405.254 15556 405 1133 8.80214 211 211 367.72 386.265 367 387 4.18757 7.55902 0 0 0 0 0.141389 0.631908 0 0 0 0 0 0 0 0 0 15448.4 13.9698 134.463 1.06426 0.139158 1 1 1.80343e-081 3.69879e-021 153 153 1 1 0 406.346 391.284 5.21131 2.51728 0 168076 216.196 1462.94 16.4705 0.139158 1
10 268.609 59.7478 -2 0.160152 8.66321e-036 0 0 1 1 129793 122.112 1369.65 15.5408 2 2 0 0 71 71 11755.8 399.577 11468 400 1009.16 8.72707 228 228 367.539 387.268 367 387 3.90676 7.32105 0 0 0 0 -0.00335875 0.631908 0 0 0 0 0 1 0 0 0 11349.5 8.29372 119.766 1.05552 -0.00286712 1 1 1.18448e-075 2.14961e-011 153 153 1 1 0 406.346 391.284 5.21131 2.51728 0 129793 122.112 1369.65 15.5408 -0.00286712 1
11 289.926 61.4344 0 0.115506 1 82.0422 0 1 1 82.0422 57.1261 15.8769 10.6624 2 1 0 0 72 72 406.792 396.625 406.5 396 7.77489 8.28104 216 216 367.463 387.125 367.5 387.5 4.33574 8.33307 0 0 0 0 -0.0364504 0.631908 0 0 0 0 0 0 0 0 0 0.44608 5.34126 1.0085 0.996924 0.0214694 0 1 0.659193 8.43868e-007 153 153 0 0 0 406.346 391.284 5.21131 2.51728 0 7.02269 57.1261 15.8769 10.6624 0.0214694 0
12 311.165 60.6694 -0.0157561 0.205951 0.939018 0 0 1 1 78.1739 75.3886 13.1415 12.348 0 1 0 0 75 75 412.093 397.373 414 397 7.53043 8.4562 218 218 367.486 386.436 367 386 4.80996 7.61747 0 0 0 0 -0.0372675 0.631908 0 0 0 0 0 0 0 0 0 5.74775 6.08959 0.96623 0.997421 0.0233861 1 1 3.27053e-008 3.42959e-008 153 153 0 0 0 406.346 391.284 5.21131 2.51728 0 78.1739 75.3886 13.1415 12.348 0.0233861 1
13 331.886 61.8054 -2 0.160274 9.76302e-036 0 0 1 1 165164 281.296 1298.54 17.2739 0 0 0 0 72 72 15800.2 409.208 15654 409 1026.95 9.17888 211 211 368.09 386.55 368 386 4.52784 7.37829 0 0 0 0 0.0667488 0.631908 0 0 0 0 0 0 0 0 0 15393.9 17.9246 121.028 1.10072 0.0660043 1 1 1.61978e-085 1.65731e-026 153 153 1 1 0 406.346 391.284 5.21131 2.51728 0 165164 281.296 1298.54 17.2739 0.0660043 1
14 353.877 60.4959 -2 0.160222 9.28393e-036 0 0 1 1 127918 176.622 1220.73 14.4079 3 0 0 1 71 71 11831.5 403.028 11543 402 918.703 7.88846 237 237 367.502 387.561 367 387 4.34783 8.10638 0 0 0 0 0.163083 0.631908 0 0 0 0 0 0 0 0 0 11425.2 11.7444 109.031 0.958052 0.159878 1 1 1.08958e-078 9.45637e-020 153 153 1 1 0 406.346 391.284 5.21131 2.51728 0 127918 176.622 1220.73 14.4079 0.159878 1
15 374.008 62.6774 0 0.0914076 1 96.221 0 1 1 96.221 60.7543 16.8071 8.80622 0 2 0 0 74 74 406.365 397.946 406 397.5 6.94119 8.12048 208 208 366.88 387.163 367 387 4.39806 7.82429 0 0 0 0 0.0934355 0.631908 0 0 0 0 0 0 0 0 0 0.0192779 6.6622 0.910266 0.965675 0.142602 0 1 0.98314 1.11615e-009 153 153 0 1 0 406.346 391.284 5.21131 2.51728 0 0.355946 60.7543 16.8071 8.80622 0.142602 0
16 395.839 61.6048 0.158603 0.188005 0.398886 70.2438 0 1 1 70.2438 101.207 12.5974 11.6161 1 3 1 0 70 70 411.471 399.386 411.5 399 6.97973 7.59155 224 224 368.036 388.871 368 389 4.13435 7.95031 0 0 0 0 -0.0291919 0.631908 0 0 0 0 0 0 0 0 0 5.12584 8.10197 0.934587 0.929906 0.0369163 1 1 2.85555e-007 4.72747e-013 153 153 0 1 0 406.346 391.284 5.21131 2.51728 0 69.0918 101.207 12.5974 11.6161 0.0369163 1
17 416.71 63.1413 -2 0.160299 1.00056e-035 0 0 1 1 170250 316.571 1455.13 20.0197 1 1 0 0 74 74 16400.2 411.297 16228 410.5 1175.93 10.7458 210 210 367.424 388.233 368 388 3.7819 7.53669 0 0 0 0 -0.130387 0.631908 0 0 0 0 0 0 0 0 0 15993.9 20.0136 136.699 1.26564 -0.128377 1 1 8.27925e-085 7.01629e-026 153 153 1 1 0 406.346 391.284 5.21131 2.51728 0 170250 316.571 1455.13 20.0197 -0.128377 1
18 438.125 61.0338 -2 0.160264 9.66634e-036 0 0 1 1 129655 212.325 1134.29 18.5172 2 0 0 0 68 68 12125.2 405.235 11920.5 404 845.417 9.89213 234 234 367.432 389.996 367 390.5 4.0029 7.78769 0 0 0 0 0.233708 0.631908 0 0 0 0 0 0 0 1 0 11718.8 13.9516 102.523 1.21674 0.230848 1 1 1.56682e-078 8.29402e-018 153 153 1 1 0 406.346 391.284 5.21131 2.51728 0 129655 212.325 1134.29 18.5172 0.230848 1
19 459.039 63.1339 0 0.106074 1 77.7675 0 1 1 77.7675 64.6658 13.7925 11.9957 1 1 2 0 67 67 407.448 397.015 407 398 6.73364 8.54133 225 225 368.364 388.733 368 388 4.36612 8.04896 0 0 0 0 0.0449302 0.631908 0 0 0 0 0 0 0 0 0 1.10217 5.73118 0.924255 1.06315 0.0943896 0 1 0.235829 8.69467e-007 153 153 0 0 0 406.346 391.284 5.21131 2.51728 0 16.4476 64.6658 13.7925 11.9957 0.0943896 0
20 480.468 62.0968 0.036374 0.160532 0.820748 0 0 1 1 96.3358 104.752 11.71 15.7933 3 0 1 0 71 71 413.634 399.507 414 399 6.56667 10.3052 225 225 368.724 389.191 368 389 4.64687 8.25021 0 0 0 0 0.0806814 0.631908 0 0 0 0 0 0 0 1 0 7.28822 8.2233 0.885913 1.23981 0.119339 1 1 3.77023e-013 4.74205e-009 153 153 0 1 0 406.346 391.284 5.21131 2.51728 0 96.3358 104.752 11.71 15.7933 0.119339 1

Total number of rows: 22575

Table truncated, full table size 8820 Kbytes.




Supplementary data files not provided
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