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Sample GSM14689 Query DataSets for GSM14689
Status Public on Jan 09, 2004
Title Morula replication 3
Sample type RNA
 
Channel 1
Source name Morula
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name Universal Control
Organism Mus musculus
Extracted molecule total RNA
 
 
Description Morula replication 3
Keywords = preimplantation
Keywords = development
 
Submission date Dec 30, 2003
Last update date May 28, 2005
Contact name Minoru S.H. Ko
E-mail(s) kom@mail.nih.gov
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(r) background (selected by user)
rPValFeatEqBG P-value from t-test of significance between r Mean signal and g(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 71.186 71.067 -1.87706 0.152236 6.253e-035 0 0 1 1 19647.1 260.761 215.802 20.1357 1 0 0 0 71 71 12576.4 417.225 12284 416 1113.86 12.6041 219 219 417.233 392.283 417 392 8.89983 9.11256 0 0 0 0 0.230123 0.609417 0 0 0 0 1 0 0 0 0 12035.4 19.7098 132.196 1.52197 0.227056 1 1 1.8876e-074 8.26001e-021 155 155 1 1 0 540.996 397.516 13.055 3.49697 0 19647.1 260.761 215.802 20.1357 0.227056 1
2 92.349 69.4574 -2 0.161241 2.49218e-035 0 0 1 1 17260 126.757 243.187 15.5835 0 1 0 0 75 75 10599.6 407.587 10386 406 1227.31 10.443 214 214 418.29 391.243 418 392 8.19597 8.70631 0 0 0 0 0.444377 0.609417 0 0 0 0 0 0 0 0 0 10058.6 10.0711 141.722 1.23814 0.433802 1 1 8.11011e-070 3.75212e-012 155 155 1 1 0 540.996 397.516 13.055 3.49697 0 17260 126.757 243.187 15.5835 0.433802 1
3 113.677 71.5155 0 0.13843 1 60.1091 16.4032 1 1 60.1091 16.4032 9.27302 5.40499 1 0 0 0 75 75 517.28 397.773 514 399 14.8911 9.67802 220 220 417.514 390.468 417.5 389 8.71019 9.51394 0 0 0 0 0.272186 0.609417 0 0 0 0 0 0 0 0 0 -23.7164 0.257777 2.01399 1.15228 0.302719 0 0 2.91219e-022 0.82353 155 155 0 0 0 540.996 397.516 13.055 3.49697 0 -109.197 1.20915 9.27302 5.40499 0.302719 0
4 134.488 70.5563 0 0.141969 1 47.9711 20.5537 1 1 47.9711 20.5537 8.66657 6.2572 0 0 2 0 74 74 541.257 399.568 538.5 398.5 18.1735 8.83344 203 203 417.734 390.005 417 390 9.01639 8.96776 0 0 0 0 0.111461 0.609417 0 0 0 0 0 0 0 0 0 0.260385 2.05201 2.35855 1.06459 0.167788 0 0 0.912293 0.0572908 155 155 0 0 1 540.996 397.516 13.055 3.49697 0 0.956794 12.0608 8.66657 6.2572 0.167788 0
5 155.606 71.3666 -1.86359 0.151207 6.66049e-035 0 0 1 1 20317.9 278.153 233.853 18.5691 1 0 0 0 74 74 13067.4 418.405 12893.5 418 1240.21 11.7507 215 215 419.507 388.772 419 389 8.75197 8.81742 0 0 0 0 0.378123 0.609417 0 0 0 0 0 0 0 0 0 12526.4 20.8898 144.175 1.39458 0.371257 1 1 1.90997e-075 7.97172e-025 155 155 1 1 0 540.996 397.516 13.055 3.49697 0 20317.9 278.153 233.853 18.5691 0.371257 1
6 176.928 70.3467 -2 0.1609 1.79373e-035 0 0 1 1 17927.6 94.5636 223.314 13.1946 0 1 0 2 73 73 10858.9 405.123 10863 404 1098.08 8.74634 227 227 421.137 388.96 420 390 10.7996 8.35248 0 0 0 0 0.158715 0.609417 0 0 0 0 0 0 0 0 0 10317.9 7.60773 128.524 1.06152 0.154368 1 1 3.35291e-072 2.87994e-010 155 155 1 0 0 540.996 397.516 13.055 3.49697 0 17927.6 94.5636 223.314 13.1946 0.154368 1
7 198.509 72.2453 0 0.136512 1 60.1091 16.4032 1 1 60.1091 16.4032 12.9103 4.83914 2 1 0 0 73 73 520.959 397.616 519 397 22.2189 8.4814 221 221 415.267 389.516 415 389 7.38895 8.70872 0 0 0 0 0.234287 0.609417 0 0 0 0 0 0 0 0 0 -20.0375 0.100882 2.80398 1.03165 0.271129 0 0 1.72755e-010 0.922335 155 155 0 0 0 540.996 397.516 13.055 3.49697 0 -92.2585 0.473205 12.9103 4.83914 0.271129 0
8 219.68 70.417 0.201635 0.348482 0.562853 35.003 0 1 1 35.003 55.6852 6.41605 8.96157 1 1 0 2 70 70 543.671 404.429 541.5 404 17.9966 9.00655 219 219 415.626 389.292 415 389 8.74441 9.00543 0 0 0 0 0.183911 0.609417 0 0 0 0 0 0 0 0 0 2.67506 6.91301 2.39298 1.11253 0.227379 0 1 0.266219 2.31225e-008 155 155 0 0 0 540.996 397.516 13.055 3.49697 0 7.17234 55.6852 6.41605 8.96157 0.227379 1
9 240.281 71.8509 -1.83677 0.149162 7.62293e-035 0 0 1 1 20929.5 304.784 261.122 17.8405 0 0 0 0 76 76 13547.8 420.224 13155 419 1414.66 11.3262 223 223 420.022 388.892 420 389 8.88132 8.27822 0 0 0 0 0.244978 0.609417 0 0 0 0 0 0 0 0 0 13006.8 22.7081 162.276 1.32922 0.240273 1 1 1.9624e-074 9.27507e-029 155 155 1 1 0 540.996 397.516 13.055 3.49697 0 20929.5 304.784 261.122 17.8405 0.240273 1
10 261.57 70.5702 -2 0.160747 1.54776e-035 0 0 1 1 18551.7 80.8127 202.941 14.971 1 2 0 0 74 74 11157.6 404.054 11159.5 402.5 999.008 10.1359 219 219 419.425 390.626 419 391 8.43255 8.64522 0 0 0 0 0.293873 0.609417 0 0 0 0 0 0 0 0 0 10616.6 6.5385 116.137 1.21129 0.287127 1 1 4.78854e-077 6.49738e-007 155 155 1 0 0 540.996 397.516 13.055 3.49697 0 18551.7 80.8127 202.941 14.971 0.287127 1
11 282.94 72.6067 0 0.16491 1 60.1091 16.4032 1 1 60.1091 16.4032 10.6875 5.9275 1 0 0 0 75 75 519.067 400.507 518 402 17.9341 10.67 217 217 417.719 389.963 418 390 7.61694 7.87216 0 0 0 0 0.0907795 0.609417 0 0 0 0 0 0 0 0 0 -21.9297 2.99111 2.3212 1.26367 0.140156 0 0 5.69454e-016 0.0202958 155 155 0 0 0 540.996 397.516 13.055 3.49697 0 -100.971 14.0304 10.6875 5.9275 0.140156 0
12 304.531 71.0812 0 0.129473 1 37.6892 0 1 1 37.6892 31.0194 6.42444 7.77188 2 3 0 0 71 71 542.887 401.662 539 402 16.5387 8.42775 222 222 419.441 391.311 419.5 391 8.83246 8.42522 0 0 0 0 -0.050703 0.609417 0 0 0 0 0 0 0 0 0 1.89095 4.14642 2.22533 1.03888 0.0345854 0 1 0.39729 0.000143282 155 155 0 0 0 540.996 397.516 13.055 3.49697 0 5.4591 31.0194 6.42444 7.77188 0.0345854 0
13 325.091 72.476 -1.79433 0.14594 9.63393e-035 0 0 1 1 21137.5 339.406 250.111 19.7679 0 1 0 0 74 74 13779.1 422.608 13529 422.5 1347.45 12.3375 225 225 421.698 393.76 421 393 10.1685 8.69704 0 0 0 0 -0.0240808 0.609417 0 0 0 0 0 0 0 0 0 13238.2 25.0926 156.642 1.46145 -0.0228472 1 1 1.41503e-074 2.49898e-028 155 155 1 1 0 540.996 397.516 13.055 3.49697 0 21137.5 339.406 250.111 19.7679 -0.0228472 1
14 346.768 70.7739 -1.93341 0.156551 4.86871e-035 0 0 1 1 18810.9 219.28 240.148 16.8098 0 0 0 0 75 75 11906.4 414.32 11786 414 1256.53 10.8878 229 229 421.834 396.533 421 396 8.84707 9.34547 0 0 0 0 0.315884 0.609417 0 0 0 0 0 0 0 0 0 11365.4 16.8044 145.095 1.28821 0.309236 1 1 6.0338e-073 1.19178e-021 155 155 1 1 0 540.996 397.516 13.055 3.49697 0 18810.9 219.28 240.148 16.8098 0.309236 1
15 368.083 72.8512 0 0.0894204 1 60.1091 0 1 1 60.1091 27.1793 9.58291 4.80689 1 1 0 0 71 71 523.352 403.31 525 403 15.1489 8.3042 223 223 420.65 398.184 421 399 7.93803 8.99836 0 0 0 0 0.203982 0.609417 0 0 0 0 0 0 0 0 0 -17.6443 5.7943 2.0813 1.02477 0.25361 0 1 7.10282e-014 2.23822e-007 155 155 0 0 0 540.996 397.516 13.055 3.49697 0 -81.2394 27.1793 9.58291 4.80689 0.25361 0
16 388.809 71.7654 0.481099 0.266437 0.0709689 32.3308 0 1 1 32.3308 97.8848 5.82428 10.145 1 1 0 0 73 73 545.315 408.74 547 407 17.986 9.64513 218 218 423.193 401.495 424 402 9.62809 9.81781 0 0 0 0 0.314321 0.609417 0 0 0 0 0 0 0 1 0 4.3187 11.2242 2.35181 1.1633 0.338632 0 1 0.0690341 4.14254e-015 155 155 0 1 0 540.996 397.516 13.055 3.49697 0 10.6953 97.8848 5.82428 10.145 0.338632 1
17 409.727 72.8051 -1.667 0.136355 2.27479e-034 0 0 1 1 21119.9 454.667 260.188 19.0625 0 0 0 1 74 74 14026.1 430.486 13945 431 1429.08 11.6434 223 223 432.027 399.318 432 399 9.77122 10.0791 0 0 0 0 0.398341 0.609417 0 0 0 0 0 0 0 1 0 13485.1 32.9709 166.13 1.38235 0.390805 1 1 2.61097e-073 6.11804e-038 155 155 1 1 0 540.996 397.516 13.055 3.49697 0 21119.9 454.667 260.188 19.0625 0.390805 1
18 431.035 71.6044 -1.83334 0.148908 7.8206e-035 0 0 1 1 18949.1 278.13 240.419 17.3068 0 0 0 0 76 76 12169.9 418.5 12008.5 417.5 1286.22 11.117 220 220 430.673 401.191 429 401 10.83 8.69472 0 0 0 0 0.276166 0.609417 0 0 0 0 0 0 0 1 0 11628.9 20.9844 147.543 1.30577 0.270626 1 1 6.80406e-074 4.08764e-027 155 155 1 1 0 540.996 397.516 13.055 3.49697 0 18949.1 278.13 240.419 17.3068 0.270626 1
19 452.535 73.471 0.0749304 0.239207 0.754095 60.1091 0 1 1 60.1091 71.4284 11.5432 6.23494 1 1 0 0 74 74 529.108 412.743 528 412 19.5893 11.1761 203 203 426.7 404.921 426 404 10.2929 10.2273 0 0 0 0 0.191968 0.609417 0 0 0 0 0 1 0 1 0 -11.8883 15.2277 2.50704 1.32921 0.224296 0 1 6.69065e-006 1.54589e-018 155 155 0 1 0 540.996 397.516 13.055 3.49697 0 -54.7371 71.4284 11.5432 6.23494 0.224296 1
20 473.47 71.9451 0.817211 0.192742 2.23592e-005 29.4599 0 1 1 29.4599 193.393 5.43402 12.1376 1 2 0 0 72 72 548.903 417.722 548.5 416.5 18.3941 10.4938 209 209 425.737 407.507 426 407 8.73667 9.91896 0 0 0 0 0.194683 0.609417 0 0 0 0 0 1 0 1 0 7.90641 20.2067 2.40806 1.2682 0.229678 1 1 0.00139242 2.64324e-026 155 155 0 1 0 540.996 397.516 13.055 3.49697 0 17.8416 193.393 5.43402 12.1376 0.229678 1

Total number of rows: 22575

Table truncated, full table size 8779 Kbytes.




Supplementary data files not provided
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