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Sample GSM14710 Query DataSets for GSM14710
Status Public on Jan 09, 2004
Title 43h-AM replication 1
Sample type RNA
 
Channel 1
Source name 43h-AM, 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-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 93.4137 80.0887 -2 0.160249 9.53236e-036 0 0 1 1 236223 366.83 2967.16 16.367 2 2 0 0 71 71 20143.4 429.239 19365 430 2088.14 11.9109 217 217 373.733 394.046 374 394 4.74268 7.48688 0 0 0 0 0.0536096 0.401867 0 0 0 0 0 0 0 1 0 19729.3 31.93 247.817 1.42464 0.053242 1 1 2.10281e-070 3.01279e-034 145 145 1 1 0 414.05 397.309 2.92322 2.13424 0 236223 366.83 2967.16 16.367 0.053242 1
2 114.281 79.3822 -2 0.160154 8.68355e-036 0 0 1 1 206206 197.799 3235 12.8346 0 1 0 0 73 73 16372.2 415.89 15765 415 2139.02 10.1893 231 231 372.922 393.056 373 393 4.45294 8.17798 0 0 0 0 0.00259126 0.401867 1 0 0 0 0 0 0 1 0 15958.1 18.581 250.354 1.20566 0.00262039 1 1 4.42535e-065 5.61185e-025 145 145 1 1 0 414.05 397.309 2.92322 2.13424 0 206206 197.799 3235 12.8346 0.00262039 1
3 135.204 80.102 0.095621 0.209276 0.647733 0 0 1 1 67.5152 84.1439 11.8105 10.4654 0 0 0 1 71 71 418.986 405.676 419 406 6.98262 8.64006 225 225 373.111 392.667 373 392 4.47823 8.07222 0 0 0 0 -0.124866 0.401867 0 0 0 0 0 0 0 0 0 4.93628 8.3666 0.86351 1.04059 -0.0988362 1 1 1.69434e-007 1.06796e-011 145 145 0 1 0 414.05 397.309 2.92322 2.13424 0 67.5152 84.1439 11.8105 10.4654 -0.0988362 1
4 156.879 80.4444 -0.0834009 0.216817 0.700489 0 0 1 1 79.9481 65.9792 13.7516 10.5959 2 1 0 0 72 72 419.903 403.861 420 404 8.29077 8.8003 226 226 373.699 391.619 373 391 4.20874 7.73772 0 0 0 0 -0.00810236 0.401867 0 0 0 0 0 0 0 0 0 5.85314 6.55165 1.00678 1.05216 0.0085721 1 1 1.20333e-007 2.49201e-008 145 145 0 1 0 414.05 397.309 2.92322 2.13424 0 79.9481 65.9792 13.7516 10.5959 0.0085721 1
5 178.031 80.4532 -2 0.160196 9.04998e-036 0 0 1 1 249810 305.473 3403.8 12.1292 2 2 0 2 70 70 21022.5 424.229 20396.5 423.5 2349.36 8.8189 221 221 373.158 391.226 373 391 4.34713 8.13262 0 0 0 0 0.102986 0.401867 0 0 0 0 0 0 0 0 0 20608.5 26.9191 280.802 1.06886 0.101618 1 1 3.18855e-067 1.03357e-037 145 145 1 1 0 414.05 397.309 2.92322 2.13424 0 249810 305.473 3403.8 12.1292 0.101618 1
6 198.62 79.7329 -2 0.160117 8.37061e-036 0 0 1 1 217782 158.118 3201.37 12.6935 1 0 0 0 73 73 16976.2 412.425 16376 412 2080.13 10.2563 209 209 372.187 389.589 372 389 3.70792 6.88596 0 0 0 0 0.0769082 0.401867 1 0 0 0 0 0 0 0 0 16562.1 15.1152 243.461 1.21343 0.0761419 1 1 4.40649e-067 5.87e-020 145 145 1 1 0 414.05 397.309 2.92322 2.13424 0 217782 158.118 3201.37 12.6935 0.0761419 1
7 219.98 80.703 0.0822734 0.360014 0.819235 39.1092 0 1 1 39.1092 47.2664 11.178 9.5144 0 1 0 0 75 75 416.773 401.907 417 402 6.92347 7.86572 224 224 372.92 389.839 373 390 4.01039 7.16626 0 0 0 0 -0.0735966 0.401867 0 0 0 0 0 0 0 0 0 2.7237 4.59721 0.835499 0.925387 -0.0467538 1 1 0.00158591 3.78961e-006 145 145 0 0 0 414.05 397.309 2.92322 2.13424 0 36.4398 47.2664 11.178 9.5144 -0.0467538 1
8 241.447 80.1165 -0.254893 0.207787 0.219935 0 0 1 1 100.973 56.1453 11.5709 11.1965 1 0 0 0 74 74 421.432 402.892 421 403.5 6.97173 9.45439 223 223 372.91 389.265 373 389 4.10899 6.82978 0 0 0 0 0.0632751 0.401867 0 0 0 0 0 0 0 0 0 7.3828 5.58244 0.846024 1.11325 0.0781999 1 1 1.72456e-013 3.33168e-006 145 145 0 1 0 414.05 397.309 2.92322 2.13424 0 100.973 56.1453 11.5709 11.1965 0.0781999 1
9 262.794 80.5284 -2 0.160175 8.86353e-036 0 0 1 1 257547 280.86 3370.38 13.7523 2 0 0 0 74 74 21550.2 422.189 20959 422 2379.38 10.3681 224 224 373.179 389.402 373 389 4.27888 7.21292 0 0 0 0 0.085425 0.401867 0 0 0 0 0 0 0 0 0 21136.1 24.8797 276.597 1.21823 0.0845674 1 1 2.05922e-071 1.24793e-032 145 145 1 1 0 414.05 397.309 2.92322 2.13424 0 257547 280.86 3370.38 13.7523 0.0845674 1
10 283.536 80.0091 -2 0.160115 8.35893e-036 0 0 1 1 220575 158.198 3308.76 12.2134 3 2 0 1 68 68 17211.4 412.412 16700 410.5 2077.8 9.50292 230 230 372.922 389.804 373 390 4.39263 7.24379 0 0 0 0 0.0950529 0.401867 0 0 0 0 0 0 0 0 0 16797.3 15.1023 251.97 1.16595 0.094007 1 1 5.5645e-063 2.76744e-020 145 145 1 1 0 414.05 397.309 2.92322 2.13424 0 220575 158.198 3308.76 12.2134 0.094007 1
11 305.121 80.6061 0.0226145 0.386809 0.953379 38.9873 0 1 1 38.9873 41.0712 12.4472 10.9397 1 1 0 0 72 72 416.694 401.292 417 401 7.64648 8.87382 230 230 373.322 390.422 373 391 4.4849 7.73697 0 0 0 0 -0.140232 0.401867 0 0 0 0 0 0 0 0 0 2.64481 3.98221 0.933273 1.0607 -0.116035 1 1 0.00579513 0.000340552 145 145 0 0 0 414.05 397.309 2.92322 2.13424 0 35.2741 41.0712 12.4472 10.9397 -0.116035 1
12 326.229 80.7048 -0.36546 0.215177 0.0894295 0 0 1 1 109.305 47.1174 13.3356 9.34239 1 4 0 0 72 72 422.056 401.986 423 403 8.02792 7.72319 218 218 372.844 390.39 372 390 4.29913 7.27722 0 0 0 0 0.0215933 0.401867 0 0 0 0 0 0 0 0 0 8.00592 4.67665 0.976749 0.927283 0.0396209 1 1 3.2057e-012 2.99888e-006 145 145 1 0 0 414.05 397.309 2.92322 2.13424 0 109.305 47.1174 13.3356 9.34239 0.0396209 1
13 347.473 80.7927 -2 0.160223 9.29106e-036 0 0 1 1 249145 346.313 2873.68 16.9449 3 0 0 0 73 73 21214.3 427.466 20874 427 2049.82 12.5156 211 211 373.166 391.37 373 391 4.57904 7.35468 0 0 0 0 -0.209028 0.401867 0 0 0 0 0 0 0 0 0 20800.2 30.1563 239.914 1.47553 -0.207465 1 1 1.41796e-074 3.4878e-032 145 145 1 1 0 414.05 397.309 2.92322 2.13424 0 249145 346.313 2873.68 16.9449 -0.207465 1
14 367.359 80.8911 -2 0.160129 8.47162e-036 0 0 1 1 216202 173.458 3091.42 11.6812 1 3 0 0 71 71 17000.6 413.746 16572 413 1998.4 9.2067 221 221 373.299 391.566 373 391 4.43452 6.90991 0 0 0 0 0.113942 0.401867 0 0 0 0 0 0 0 0 0 16586.5 16.437 237.166 1.10692 0.112537 1 1 1.6369e-066 7.46244e-024 145 145 1 1 0 414.05 397.309 2.92322 2.13424 0 216202 173.458 3091.42 11.6812 0.112537 1
15 388.979 82.0928 0.171673 0.294586 0.560055 0 0 1 1 43.1419 64.0578 15.3111 12.0501 0 0 0 0 69 69 417.246 403.594 415 403 9.20583 9.70948 221 221 372.154 392.014 372 391 4.25909 7.29351 0 0 0 0 0.0541121 0.401867 0 0 0 0 0 0 0 0 0 3.19674 6.28475 1.13453 1.18225 0.0651527 1 1 0.00618815 1.16498e-006 145 145 0 1 0 414.05 397.309 2.92322 2.13424 0 43.1419 64.0578 15.3111 12.0501 0.0651527 1
16 409.832 81.6737 -0.157717 0.17357 0.363529 0 0 1 1 110.26 76.6836 11.6853 10.5791 3 1 1 1 70 70 422.057 404.986 422 404 6.80342 8.73522 225 225 372.92 391.724 373 392 4.30457 7.33354 0 0 0 0 -0.0977759 0.401867 0 0 0 0 0 0 0 0 0 8.00751 7.67626 0.848628 1.059 -0.0731284 1 1 1.0304e-014 3.59336e-010 145 145 1 1 0 414.05 397.309 2.92322 2.13424 0 110.26 76.6836 11.6853 10.5791 -0.0731284 1
17 431.507 82.1808 -2 0.160246 9.50177e-036 0 0 1 1 255439 391.513 3302.93 17.5534 2 1 0 0 75 75 22036.8 430.933 21288 431 2421.32 12.965 222 222 373.153 391.847 373 391 4.00271 7.85583 0 0 0 0 0.023304 0.401867 0 0 0 0 0 0 0 0 0 21622.7 33.6239 279.59 1.50752 0.0231834 1 1 1.55451e-072 4.13993e-035 145 145 1 1 0 414.05 397.309 2.92322 2.13424 0 255439 391.513 3302.93 17.5534 0.0231834 1
18 452.828 81.531 -2 0.160177 8.88159e-036 0 0 1 1 218018 240.448 3069.46 14.3084 3 0 0 0 73 73 17732.3 419.315 17153 421 2083.22 11.0854 224 224 373.679 392.446 373 392 4.55896 7.46152 0 0 0 0 0.161028 0.401867 0 0 0 0 0 0 0 0 0 17318.2 22.0056 243.822 1.30949 0.1596 1 1 2.06111e-068 4.31921e-027 145 145 1 1 0 414.05 397.309 2.92322 2.13424 0 218018 240.448 3069.46 14.3084 0.1596 1
19 473.695 82.0381 0.0100262 0.256055 0.968766 0 0 1 1 60.3993 61.8099 14.0179 11.1654 0 0 0 0 76 76 418.5 403.408 418.5 404 8.75214 9.47865 217 217 373.152 393.493 373 393 4.24154 7.61281 0 0 0 0 0.155982 0.401867 0 0 0 0 0 0 0 1 0 4.45037 6.09844 1.03287 1.10163 0.164833 1 1 4.44109e-005 3.91003e-007 145 145 0 1 0 414.05 397.309 2.92322 2.13424 0 60.3993 61.8099 14.0179 11.1654 0.164833 1
20 495.155 82.0722 -0.124333 0.163968 0.448288 0 0 1 1 113.065 84.9173 11.7632 10.2303 2 0 0 0 70 70 422.243 405.829 422 407 6.83647 8.45786 221 221 373.38 393.122 373 393 4.85427 8.62705 0 0 0 0 -0.0090447 0.401867 0 0 0 0 0 0 0 1 0 8.19322 8.51912 0.852413 1.02633 0.0112244 1 1 4.68856e-015 3.73833e-012 145 145 1 1 0 414.05 397.309 2.92322 2.13424 0 113.065 84.9173 11.7632 10.2303 0.0112244 1

Total number of rows: 22575

Table truncated, full table size 8791 Kbytes.




Supplementary data files not provided
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