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Sample GSM14713 Query DataSets for GSM14713
Status Public on Jan 09, 2004
Title 54h-AM replication 1
Sample type RNA
 
Channel 1
Source name 54h-AM, late 2-cell embryo
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name Universal Reference
Organism Mus musculus
Extracted molecule total RNA
 
 
Description 54h-AM 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) [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 82.3565 78.7059 -2 0.160067 7.97542e-036 0 0 1 1 403011 169.231 5988.06 10.8682 0 1 0 0 73 73 18809.1 414.849 17982 416 2335.84 9.13581 216 216 373.657 393.903 373 394 4.68776 7.75825 0 0 0 0 0.192921 0.16965 1 0 0 0 0 0 0 1 0 18399.8 16.8156 273.389 1.07991 0.191041 1 1 9.42181e-067 3.4402e-025 150 150 1 1 0 409.329 398.034 3.21826 1.85271 0 403011 169.231 5988.06 10.8682 0.191041 1
2 102.894 78.2441 -2 0.160036 7.73237e-036 0 0 1 1 419977 93.7114 11421.8 9.92293 0 2 0 0 72 72 18224.9 408.056 17772 408 4111.25 8.91255 226 226 373.677 393.009 373.5 393 4.44793 8.07795 0 0 0 0 0.150846 0.16965 1 0 0 0 0 0 0 0 0 17815.6 10.0218 484.515 1.06119 0.149318 1 1 5.8374e-048 2.43621e-014 150 150 1 1 0 409.329 398.034 3.21826 1.85271 0 419977 93.7114 11421.8 9.92293 0.149318 1
3 124.188 78.9063 -0.315143 0.158543 0.0468404 0 0 1 1 144.961 70.1631 17.6534 13.7023 2 0 0 0 70 70 416.971 404.071 417.5 404 7.46969 9.78363 225 225 374.044 392.978 374 394 4.54421 7.66861 0 0 0 0 0.0642813 0.16965 0 0 0 0 0 0 0 0 0 7.64219 6.03768 0.930665 1.17911 0.0673015 1 1 2.83307e-012 2.48605e-006 150 150 0 1 0 409.329 398.034 3.21826 1.85271 0 144.961 70.1631 17.6534 13.7023 0.0673015 1
4 145.719 78.9688 -0.390981 0.148999 0.00868902 0 0 1 1 169.117 68.7397 19.1727 11.0689 0 1 0 1 74 74 418.149 404.014 418 402 8.29868 8.18032 222 222 372.815 393.383 372.5 393 4.1746 7.42823 0 0 0 0 0.0447672 0.16965 0 0 0 0 0 0 0 1 0 8.81941 5.97976 0.999848 0.9629 0.0496617 1 1 1.36119e-013 2.51685e-008 150 150 1 1 0 409.329 398.034 3.21826 1.85271 0 169.117 68.7397 19.1727 11.0689 0.0496617 1
5 166.927 79.2923 -2 0.160057 7.89518e-036 0 0 1 1 434434 154.527 6644.73 11.1184 0 0 0 1 74 74 20204.2 413.419 19487.5 413.5 2604.49 9.43326 225 225 372.782 392.782 373 393 4.49917 8.22353 0 0 0 0 0.266455 0.16965 1 0 0 0 0 0 0 0 0 19794.9 15.3852 302.766 1.10698 0.263975 1 1 1.54006e-066 1.53293e-022 150 150 1 1 0 409.329 398.034 3.21826 1.85271 0 434434 154.527 6644.73 11.1184 0.263975 1
6 187.72 78.5 -2 0.160019 7.60735e-036 0 0 1 1 444310 53.1076 11848.5 7.20377 0 2 0 1 73 73 17988 404.123 17356 405 4005.2 6.93811 228 228 373.096 390.711 373 391 4.41756 7.54397 0 0 0 0 0.035219 0.16965 1 0 0 0 0 0 0 0 0 17578.6 6.08954 468.774 0.826014 0.0346408 1 1 5.44471e-049 1.62477e-010 150 150 1 1 0 409.329 398.034 3.21826 1.85271 0 444310 53.1076 11848.5 7.20377 0.0346408 1
7 209 79.549 0.0151904 0.270876 0.955279 0 0 1 1 56.6396 58.6558 15.5167 10.8375 0 2 0 1 71 71 412.606 402.634 413 403 7.23183 7.04727 223 223 372.7 389.466 372 390 4.41071 7.1878 0 0 0 0 -0.230203 0.16965 0 0 0 0 0 0 0 0 0 3.27639 4.60005 0.897585 0.849927 -0.207763 1 1 0.000455856 7.24285e-007 150 150 0 0 0 409.329 398.034 3.21826 1.85271 0 56.6396 58.6558 15.5167 10.8375 -0.207763 1
8 230.069 79.4216 -0.487821 0.212114 0.0214591 0 0 1 1 125.78 40.9065 18.6741 12.5289 0 0 0 0 75 75 416.347 401.36 417 401 8.73095 8.72499 223 223 373.152 390.39 373 391 4.39534 7.29651 0 0 0 0 0.142384 0.16965 0 0 0 0 0 0 0 0 0 7.01742 3.32625 1.04185 1.01877 0.142607 1 1 1.88976e-009 0.00163219 150 150 0 0 0 409.329 398.034 3.21826 1.85271 0 125.78 40.9065 18.6741 12.5289 0.142607 1
9 251.303 79.6567 -2 0.160056 7.88397e-036 0 0 1 1 428228 148.44 6000.46 11.2262 0 0 0 1 73 73 19783.9 412.918 19259 413 2319.55 9.53029 228 228 373.732 390.675 374 390 4.2065 8.35606 0 0 0 0 -0.0249112 0.16965 0 0 0 0 0 0 0 0 0 19374.6 14.8841 271.483 1.12565 -0.0246631 1 1 1.4717e-068 3.00956e-021 150 150 1 1 0 409.329 398.034 3.21826 1.85271 0 428228 148.44 6000.46 11.2262 -0.0246631 1
10 272.05 79.2733 -2 0.160027 7.66806e-036 0 0 1 1 418987 71.2378 7067.99 8.9947 0 1 0 0 74 74 17522.9 405.946 17922 405 2483.43 8.49479 223 223 373.054 391.462 373 391 4.38638 7.48735 0 0 0 0 0.0925205 0.16965 1 0 0 0 0 0 0 0 0 17113.6 7.9122 288.693 0.999018 0.091477 1 1 1.72326e-063 1.51318e-011 150 150 1 1 0 409.329 398.034 3.21826 1.85271 0 418987 71.2378 7067.99 8.9947 0.091477 1
11 293.779 79.7308 0.0438625 0.243922 0.857292 0 0 1 1 61.081 67.5722 15.0381 12.569 1 2 0 2 70 70 412.8 403.429 411 404.5 6.80281 8.29977 224 224 372.487 392.246 372 391 4.11928 8.50046 0 0 0 0 0.140405 0.16965 0 0 0 0 0 0 0 0 0 3.47076 5.39482 0.854497 1.00348 0.13994 1 1 0.000109198 8.92139e-007 150 150 0 1 0 409.329 398.034 3.21826 1.85271 0 61.081 67.5722 15.0381 12.569 0.13994 1
12 314.848 79.9798 -0.59171 0.184885 0.00137223 0 0 1 1 162.705 41.6574 21.0054 13.8319 1 1 0 0 70 70 418.2 401.5 418 401.5 9.32598 9.54585 222 222 372.523 391.806 372 392 3.82974 8.06553 0 0 0 0 -0.13805 0.16965 0 0 0 0 0 0 0 0 0 8.87076 3.46625 1.14522 1.15093 -0.128085 1 1 3.18568e-011 0.00359067 150 150 1 0 0 409.329 398.034 3.21826 1.85271 0 162.705 41.6574 21.0054 13.8319 -0.128085 1
13 336.265 79.8509 -2 0.160053 7.86423e-036 0 0 1 1 437170 144.581 5055.71 12.7068 2 0 0 1 72 72 20173.8 412.542 19905 413 1939.47 10.7428 223 223 372.874 392.314 373 392 4.21948 8.00226 0 0 0 0 0.0206078 0.16965 0 0 0 0 0 0 0 0 0 19764.5 14.5079 228.569 1.27505 0.0204854 1 1 1.07883e-073 7.74815e-018 150 150 1 1 0 409.329 398.034 3.21826 1.85271 0 437170 144.581 5055.71 12.7068 0.0204854 1
14 356.5 80 -2 0.160027 7.66595e-036 0 0 1 1 421182 70.8737 9053.63 8.15897 0 0 0 0 74 74 17612.8 405.905 17040 404 3181.16 7.6859 230 230 373.678 392.378 374 392 4.27555 7.49092 0 0 0 0 -0.0605564 0.16965 1 0 0 0 0 0 0 0 0 17203.5 7.87166 369.802 0.906184 -0.0596866 1 1 5.28393e-056 4.72341e-013 150 150 1 1 0 409.329 398.034 3.21826 1.85271 0 421182 70.8737 9053.63 8.15897 -0.0596866 1
15 377.762 80.9901 -0.0074588 0.263522 0.97742 0 0 1 1 59.8178 58.7992 14.0741 14.0521 0 1 0 0 75 75 412.773 402.667 413 403 6.63849 9.4987 224 224 372.585 392.513 373 392 3.88996 7.43038 0 0 0 0 0.112582 0.16965 0 0 0 0 0 0 0 0 0 3.44409 4.63292 0.810334 1.1072 0.113016 1 1 5.12347e-005 7.53121e-005 150 150 0 0 0 409.329 398.034 3.21826 1.85271 0 59.8178 58.7992 14.0741 14.0521 0.113016 1
16 398.553 81.0194 -0.184245 0.144984 0.2038 0 0 1 1 138.806 90.8164 17.0265 10.6837 0 0 0 0 75 75 416.52 405.987 416 405 7.29191 7.99576 220 220 373.027 393.236 373 393 3.95513 7.0671 0 0 0 0 -0.250429 0.16965 0 0 0 0 0 0 0 0 0 7.19076 7.95292 0.882047 0.935582 -0.22774 1 1 2.15753e-012 1.00651e-012 150 150 0 1 0 409.329 398.034 3.21826 1.85271 0 138.806 90.8164 17.0265 10.6837 -0.22774 1
17 420.224 81.3889 -2 0.160049 7.83625e-036 0 0 1 1 448506 138.173 5814.71 9.81302 0 0 0 0 76 76 20634.3 411.934 20119.5 413 2285.89 8.50464 231 231 373.515 393.416 373 393 4.95093 8.08329 0 0 0 0 0.206531 0.16965 0 0 0 0 0 0 0 1 0 20225 13.9005 262.21 0.987208 0.204118 1 1 3.41407e-073 3.38146e-023 150 150 1 1 0 409.329 398.034 3.21826 1.85271 0 448506 138.173 5814.71 9.81302 0.204118 1
18 441.634 80.8119 -2 0.160024 7.64273e-036 0 0 1 1 495343 73.8717 11617.5 9.88266 0 0 0 0 76 76 21213 406.013 21697 405.5 4253.57 9.2123 222 222 373.189 392.324 373 392 4.64196 7.96333 0 0 0 0 0.115213 0.16965 1 0 0 0 0 0 0 0 0 20803.7 7.97941 487.918 1.0675 0.114063 1 1 2.47378e-054 9.66151e-011 150 150 1 1 0 409.329 398.034 3.21826 1.85271 0 495343 73.8717 11617.5 9.88266 0.114063 1
19 462.519 81.3679 0.0757075 0.252751 0.764533 0 0 1 1 56.7043 67.5031 16.1063 12.1499 0 0 1 0 77 77 412.571 403.39 412 403 7.745 8.35425 220 220 372.945 393.559 373 394 4.24659 7.69814 0 0 0 0 0.182585 0.16965 0 0 0 0 0 0 0 1 0 3.24219 5.35586 0.920909 0.963999 0.180422 1 1 0.000678847 3.52234e-007 150 150 0 1 0 409.329 398.034 3.21826 1.85271 0 56.7043 67.5031 16.1063 12.1499 0.180422 1
20 483.945 81.3853 -0.400154 0.18564 0.0311201 0 0 1 1 133.068 52.9566 15.6689 11.1975 1 6 2 1 66 66 416.561 402.455 416 402.5 6.57999 7.49396 222 222 372.865 391.802 373 392 4.35524 8.1904 0 0 0 0 0.171967 0.16965 0 0 0 0 0 0 0 0 0 7.23136 4.4208 0.8515 0.934764 0.16989 1 1 9.51976e-013 1.16576e-005 150 150 0 0 0 409.329 398.034 3.21826 1.85271 0 133.068 52.9566 15.6689 11.1975 0.16989 1

Total number of rows: 22575

Table truncated, full table size 8810 Kbytes.




Supplementary data files not provided
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