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Sample GSM14726 Query DataSets for GSM14726
Status Public on Jan 09, 2004
Title 43h-DMSO replication 2
Sample type RNA
 
Channel 1
Source name 43h-DMSO, 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-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 78.1608 66.7442 -2 0.160203 9.11084e-036 0 0 1 1 218417 276.29 1803.68 14.8258 1 0 0 0 73 73 13647.3 415.74 13471 415 934.248 9.77955 200 200 372.82 392.43 372 392 5.60309 8.36871 0 0 0 0 -0.0208634 0.615555 0 0 0 0 0 0 0 1 0 13241.3 21.6419 109.346 1.1613 -0.0201819 1 1 5.93101e-085 4.06192e-030 155 155 1 1 0 405.951 394.098 4.9932 2.44267 0 218417 276.29 1803.68 14.8258 -0.0201819 1
2 98.9914 64.6293 -2 0.160127 8.45491e-036 0 0 1 1 176810 139.451 1789.34 13.6667 2 0 0 0 74 74 10100.1 406.176 9943 406 843.939 10.0415 221 221 373.629 391.837 373 392 5.87118 8.29954 0 0 0 0 0.0789549 0.615555 0 0 0 0 0 0 0 0 0 9694.2 12.0778 98.1067 1.18367 0.0782792 1 1 1.73839e-079 5.78916e-016 155 155 1 1 0 405.951 394.098 4.9932 2.44267 0 176810 139.451 1789.34 13.6667 0.0782792 1
3 120.627 67.0082 -0.461806 0.162184 0.00440763 0 0 1 1 165.378 57.1046 19.9934 11.031 1 1 0 0 74 74 414.554 399.311 415 400 8.25475 8.49645 208 208 374.769 391.087 374 391 6.95983 7.59622 0 0 0 0 -0.00678588 0.615555 0 0 0 0 0 0 0 0 0 8.60278 5.21294 1.04004 1.00699 0.0401083 1 1 6.15338e-013 1.68382e-006 155 155 0 0 0 405.951 394.098 4.9932 2.44267 0 165.378 57.1046 19.9934 11.031 0.0401083 1
4 141.346 65.7795 -0.295379 0.125972 0.019037 0 0 1 1 185.709 94.0704 17.5077 10.8507 2 2 0 1 71 71 415.718 402.592 416 402 6.98403 8.08805 210 210 371.081 388.781 370 388 5.12972 7.98681 0 0 0 0 -0.132563 0.615555 0 0 0 0 0 0 0 0 0 9.76704 8.49368 0.920786 0.979721 -0.0632175 1 1 2.95158e-018 5.78732e-013 155 155 0 1 0 405.951 394.098 4.9932 2.44267 0 185.709 94.0704 17.5077 10.8507 -0.0632175 1
5 163.239 67.2819 -2 0.160183 8.93401e-036 0 0 1 1 231552 264.095 2168.15 16.9137 2 0 0 0 73 73 14464.7 414.753 14229 414 1124.72 11.1776 219 219 369.598 388.169 369 388 4.35081 8.32779 0 0 0 0 0.129879 0.615555 0 0 0 0 0 0 0 0 0 14058.7 20.6556 131.64 1.32287 0.12872 1 1 4.80032e-081 2.59107e-025 155 155 1 1 0 405.951 394.098 4.9932 2.44267 0 231552 264.095 2168.15 16.9137 0.12872 1
6 184.156 65.7482 -2 0.160092 8.16741e-036 0 0 1 1 189734 107.976 2157.87 11.6371 0 1 0 0 73 73 10611.8 403.63 10331 403 991.718 8.61605 204 204 369.525 388.186 369 389 4.29393 7.27331 0 0 0 0 -0.0724814 0.615555 0 0 0 0 0 0 0 0 0 10205.9 9.53227 116.072 1.02734 -0.0707407 1 1 5.18413e-075 3.29266e-014 155 155 1 1 0 405.951 394.098 4.9932 2.44267 0 189734 107.976 2157.87 11.6371 -0.0707407 1
7 205.213 67.0656 0 0.199304 1 114.287 22.4736 1 1 114.287 22.4736 22.0185 10.1726 0 1 0 0 72 72 409.722 394.069 409.5 394 7.41947 9.23302 212 212 370.382 388.505 370 389 5.1939 7.23177 0 0 0 0 0.150374 0.615555 0 0 0 0 0 0 0 0 0 3.77095 -0.0284227 0.961985 1.10567 0.180052 1 0 0.00016062 0.979559 155 155 0 0 0 405.951 394.098 4.9932 2.44267 0 86.3117 -0.261501 22.0185 10.1726 0.180052 0
8 226.095 65.9921 -0.590547 0.171288 0.000565425 0 0 1 1 177.539 45.5772 20.1911 11.913 1 1 0 0 67 67 415.164 398.269 415 398 7.92311 8.7777 226 226 370.774 386.717 371 386 4.35813 7.67966 0 0 0 0 -0.181904 0.615555 0 0 0 0 0 0 0 0 0 9.21291 4.17079 1.04776 1.09017 -0.122901 1 1 9.68849e-014 0.000278984 155 155 0 0 0 405.951 394.098 4.9932 2.44267 0 177.539 45.5772 20.1911 11.913 -0.122901 1
9 247.52 67.0177 -2 0.160162 8.75409e-036 0 0 1 1 236123 238.774 2095.62 15.4124 0 0 0 0 74 74 14610.6 412.946 14409 413.5 1084.48 10.3287 220 220 371.559 386.745 371 386.5 4.87854 7.83964 0 0 0 0 0.0205182 0.615555 0 0 0 0 0 0 0 0 0 14204.7 18.8481 126.068 1.21661 0.0205653 1 1 1.27592e-083 2.31985e-025 155 155 1 1 0 405.951 394.098 4.9932 2.44267 0 236123 238.774 2095.62 15.4124 0.0205653 1
10 268.284 65.6429 -2 0.160108 8.30192e-036 0 0 1 1 187434 126.126 2003.4 12.85 1 1 0 0 72 72 10637.9 405.069 10424.5 406 927.985 9.33768 217 217 370.009 387.009 369 388 4.43157 7.1976 0 0 0 0 0.293092 0.615555 0 0 0 0 0 0 0 0 0 10231.9 10.9716 109.365 1.11781 0.288937 1 1 4.20107e-076 3.95008e-015 155 155 1 1 0 405.951 394.098 4.9932 2.44267 0 187434 126.126 2003.4 12.85 0.288937 1
11 290.024 67.2063 0 0.169727 1 100.716 25.5018 1 1 100.716 25.5018 19.7846 9.12172 1 1 0 1 70 70 407.971 396.2 407.5 396 7.48907 7.12334 216 216 369.537 388.12 369 387 4.31315 7.23457 0 0 0 0 0.0468356 0.615555 0 0 0 0 0 0 0 0 0 2.02016 2.10213 0.980858 0.873717 0.0981699 0 0 0.0420976 0.0185466 155 155 0 0 0 405.951 394.098 4.9932 2.44267 0 40.748 21.9465 19.7846 9.12172 0.0981699 0
12 311.112 66.216 -0.273709 0.174062 0.11584 0 0 1 1 124.854 66.4806 17.5147 12.2275 1 4 1 0 67 67 412.433 400.179 412 400 6.67928 9.01333 216 216 370.477 388.056 371 388 3.93546 7.35269 0 0 0 0 0.187449 0.615555 0 0 0 0 0 0 0 0 0 6.48156 6.08124 0.909239 1.1185 0.213248 1 1 1.65648e-010 7.42447e-007 155 155 0 0 0 405.951 394.098 4.9932 2.44267 0 124.854 66.4806 17.5147 12.2275 0.213248 1
13 332.168 67.5493 -2 0.160194 9.0274e-036 0 0 1 1 230104 277.656 1925.69 15.8464 0 0 0 1 75 75 14446.2 415.707 14252 416 1017.57 10.5443 202 202 370.416 387.644 370 387.5 4.57392 7.77492 0 0 0 0 0.195623 0.615555 0 0 0 0 0 0 0 0 0 14040.2 21.6088 117.5 1.23326 0.193465 1 1 2.09349e-086 9.63577e-029 155 155 1 1 0 405.951 394.098 4.9932 2.44267 0 230104 277.656 1925.69 15.8464 0.193465 1
14 353.692 65.817 -2 0.160137 8.5378e-036 0 0 1 1 186782 158.965 1839.95 11.9747 0 1 0 0 76 76 10854.7 407.592 10661.5 407 897.296 8.6951 219 219 370.447 388.365 370 388 4.28361 7.82632 0 0 0 0 -0.065387 0.615555 0 0 0 0 0 0 0 0 0 10448.7 13.4942 102.928 1.01651 -0.0636941 1 1 4.67169e-082 5.20861e-022 155 155 1 1 0 405.951 394.098 4.9932 2.44267 0 186782 158.965 1839.95 11.9747 -0.0636941 1
15 374 67.904 0 0.132015 1 97.8205 0 1 1 97.8205 48.1591 17.5739 11.4749 0 1 2 2 64 64 409.5 398.578 409 397 6.41922 8.39464 201 201 371.09 388.965 371 389 4.80853 7.5567 0 0 0 0 -0.102065 0.615555 0 0 0 0 0 0 0 0 0 3.54873 4.48026 0.897051 1.06751 -0.03916 1 1 0.000146002 8.09407e-005 155 155 0 0 0 405.951 394.098 4.9932 2.44267 0 69.5223 48.1591 17.5739 11.4749 -0.03916 0
16 395.415 66.6504 -0.30541 0.152619 0.0453779 0 0 1 1 149.778 74.1374 19.7245 12.1068 1 1 2 0 72 72 413.764 400.847 414 400 8.0395 9.20297 219 219 370.562 389.023 370 389 4.08843 7.79581 0 0 0 0 0.174831 0.615555 0 0 0 0 0 0 0 0 0 7.81262 6.74936 1.02885 1.10218 0.201143 1 1 1.91422e-011 3.76996e-008 155 155 0 1 0 405.951 394.098 4.9932 2.44267 0 149.778 74.1374 19.7245 12.1068 0.201143 1
17 416.524 68.4802 -2 0.160184 8.93793e-036 0 0 1 1 237238 271.262 2065.4 17.0373 0 3 0 0 73 73 14893.3 415.192 14723 415 1077.63 11.1948 201 201 370.677 389.955 371 390 4.38519 6.69051 0 0 0 0 -0.124961 0.615555 0 0 0 0 0 0 0 0 0 14487.4 21.0939 126.128 1.32486 -0.123292 1 1 2.61536e-083 8.39586e-026 155 155 1 1 0 405.951 394.098 4.9932 2.44267 0 237238 271.262 2065.4 17.0373 -0.123292 1
18 437.326 67.0078 -2 0.160149 8.63797e-036 0 0 1 1 184916 171.084 2002.95 13.9368 4 2 0 0 71 71 10821.8 408.521 10623 409 950.639 9.76123 223 223 370.121 389.48 370 389 4.86194 7.00889 0 0 0 0 0.0748768 0.615555 0 0 0 0 0 0 0 0 0 10415.8 14.4233 112.821 1.17494 0.0741904 1 1 7.25967e-075 1.5781e-019 155 155 1 1 0 405.951 394.098 4.9932 2.44267 0 184916 171.084 2002.95 13.9368 0.0741904 1
19 459.403 68.4958 0 0.106351 1 98.023 0 1 1 98.023 44.1465 18.3201 9.31183 0 1 0 0 75 75 409.467 398.213 409 398 7.29741 7.32322 216 216 369.532 389.782 369 389 4.51961 6.96128 0 0 0 0 0.212546 0.615555 0 0 0 0 0 0 0 0 0 3.5154 4.11547 0.933211 0.868076 0.246742 1 1 0.00026876 8.83865e-006 155 155 0 0 0 405.951 394.098 4.9932 2.44267 0 69.0118 44.1465 18.3201 9.31183 0.246742 0
20 480.466 67.8343 -0.178757 0.123578 0.148034 0 0 1 1 166.296 110.186 18.4641 13.2831 1 0 1 0 74 74 414.703 404.041 415 403.5 7.61349 10.1717 209 209 369.727 390.292 370 390 4.2593 6.9501 0 0 0 0 0.155466 0.615555 0 0 0 0 0 0 0 0 0 8.75143 9.94267 0.971682 1.19861 0.181284 1 1 1.11072e-014 2.73325e-012 155 155 0 1 0 405.951 394.098 4.9932 2.44267 0 166.296 110.186 18.4641 13.2831 0.181284 1

Total number of rows: 22575

Table truncated, full table size 8804 Kbytes.




Supplementary data files not provided
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