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Sample GSM14692 Query DataSets for GSM14692
Status Public on Jan 09, 2004
Title Blastocyst replication 2
Sample type RNA
 
Channel 1
Source name Blastocyst
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name Universal Control
Organism Mus musculus
Extracted molecule total RNA
 
 
Description Blastocyst 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(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 65.0768 59.6399 -1.97484 0.159752 4.20209e-035 0 0 1 1 15585.8 165.156 200.473 17.6084 3 1 0 2 70 70 10920.3 407.429 10598.5 407.5 1120.73 10.0788 218 218 416.119 389.44 416 390 8.75496 7.48692 0 0 0 0 0.106907 0.699402 0 0 0 0 1 0 0 0 0 10414.7 11.5322 133.959 1.22953 0.106119 1 1 6.12206e-069 2.89824e-014 156 156 1 1 0 505.613 395.896 16.4965 3.07375 0 15585.8 165.156 200.473 17.6084 0.106119 1
2 86.1261 61 -2 0.160816 1.6547e-035 0 0 1 1 12700.4 56.6793 189.359 15.2546 2 1 0 0 67 67 8690.51 400 8372 401 998.832 8.81287 214 214 417.439 389.486 418 389 8.63901 7.97162 0 0 0 0 0.056521 0.699402 0 0 0 0 0 0 0 0 0 8184.89 4.10358 122.034 1.10443 0.0567834 1 1 1.85215e-062 0.000394278 156 156 1 0 0 505.613 395.896 16.4965 3.07375 0 12700.4 56.6793 189.359 15.2546 0.0567834 1
3 107.8 60.0903 0 0.155705 1 39.6112 27.4353 1 1 39.6112 27.4353 4.75849 9.72232 4 0 1 0 67 67 491.582 396.672 492 396 12.0933 8.68539 211 211 412.246 387.891 412 387 7.79291 8.79082 0 0 0 0 0.040507 0.699402 0 0 0 0 0 0 0 0 0 -14.0308 0.775225 1.98173 1.08925 0.134733 0 0 3.75244e-011 0.478911 156 156 0 0 0 505.613 395.896 16.4965 3.07375 0 -33.6905 6.91941 4.75849 9.72232 0.134733 0
4 128.409 60.9623 0.227563 0.318671 0.475165 0 0 1 1 37.1527 62.7413 3.64456 12.3689 4 1 0 1 70 70 526.514 401.1 525 400.5 13.1212 8.33214 221 221 414.19 388.787 413 388 9.50981 7.8558 0 0 0 0 0.175698 0.699402 0 0 0 0 0 0 0 0 0 20.9014 5.20358 2.05036 1.02584 0.238546 1 1 3.16571e-019 2.61403e-006 156 156 0 0 0 505.613 395.896 16.4965 3.07375 0 37.1527 62.7413 3.64456 12.3689 0.238546 1
5 150.088 60.2987 -1.95566 0.158275 4.51592e-035 0 0 1 1 15993.2 177.123 180.146 16.6272 2 1 0 0 72 72 11228.9 408.222 11037 408.5 1024.85 9.59346 221 221 420.385 389.389 420 389 11.0252 7.41023 0 0 0 0 0.0375024 0.699402 0 0 0 0 1 0 0 0 0 10723.3 12.3258 120.786 1.15707 0.0382688 1 1 1.63741e-074 7.35673e-017 156 156 1 1 0 505.613 395.896 16.4965 3.07375 0 15993.2 177.123 180.146 16.6272 0.0382688 1
6 171.148 61.5 -2 0.160885 1.76904e-035 0 0 1 1 13781.7 68.6126 212.647 17.2794 1 1 0 1 73 73 9438.34 400.836 9175 400 1177.56 10.4177 218 218 418.757 388.248 417 389 10.1241 7.97653 0 0 0 0 0.256027 0.699402 1 0 0 0 0 0 0 0 0 8932.73 4.9392 137.829 1.24389 0.252281 1 1 1.33762e-065 0.000158485 156 156 1 0 0 505.613 395.896 16.4965 3.07375 0 13781.7 68.6126 212.647 17.2794 0.252281 1
7 192.288 60.4172 0 0.132197 1 39.6112 27.4353 1 1 39.6112 27.4353 5.21406 8.35247 2 2 0 1 71 71 481.07 393.592 481 394 14.5232 7.60747 219 219 413.872 387.886 415 388 8.30232 8.75197 0 0 0 0 0.136676 0.699402 0 0 0 0 0 0 0 0 0 -24.5425 -2.30487 2.17145 0.935781 0.216544 0 0 6.66623e-022 0.015907 156 156 0 0 1 505.613 395.896 16.4965 3.07375 0 -58.9309 -20.5725 5.21406 8.35247 0.216544 0
8 213.298 60.7453 0 0.107299 1 0 34.9796 1 1 34.6562 34.9796 4.50787 8.59644 0 5 0 3 68 68 524.015 396.868 523 396 16.4612 5.88929 213 213 415.122 387.268 415 387 9.04466 8.95053 0 0 0 0 0.16337 0.699402 0 0 0 0 0 0 0 0 0 18.4018 0.971231 2.3936 0.755393 0.254544 1 0 3.46892e-012 0.202098 156 156 0 0 0 505.613 395.896 16.4965 3.07375 0 34.6562 11.0527 4.50787 8.59644 0.254544 0
9 234.721 61.0389 -1.82977 0.148653 8.10299e-035 0 0 1 1 16036.3 237.323 198.569 19.8357 2 3 0 0 71 71 11380.4 412.225 11097 414 1134.58 11.3114 216 216 421.505 388.417 421 388 10.1624 8.96466 0 0 0 0 0.0508042 0.699402 0 0 0 0 0 0 0 0 0 10874.8 16.3289 134.656 1.36479 0.051206 1 1 7.62462e-071 4.85768e-019 156 156 1 1 0 505.613 395.896 16.4965 3.07375 0 16036.3 237.323 198.569 19.8357 0.051206 1
10 255.804 61.7255 -2 0.16085 1.70922e-035 0 0 1 1 15513.1 75.4987 297.056 17.1443 1 2 0 0 73 73 10616.3 401.301 10093 401 1654.13 10.2736 209 209 419.297 388.775 418 389 9.57451 8.45134 0 0 0 0 0.119203 0.699402 1 0 0 0 0 0 0 0 0 10110.6 5.40495 193.606 1.22736 0.117736 1 1 5.54647e-059 3.34131e-005 156 156 1 0 0 505.613 395.896 16.4965 3.07375 0 15513.1 75.4987 297.056 17.1443 0.117736 1
11 277.248 60.9814 0 0.133048 1 39.6112 27.4353 1 1 39.6112 27.4353 4.33506 8.43668 1 1 0 0 74 74 489.054 394.365 488 394.5 10.588 7.85062 224 224 414.83 387.808 414 387 8.51365 8.07386 0 0 0 0 0.0839724 0.699402 0 0 0 0 0 0 0 0 0 -16.5588 -1.53155 1.80539 0.945215 0.188493 0 0 4.64711e-017 0.108921 156 156 0 0 1 505.613 395.896 16.4965 3.07375 0 -39.7608 -13.6701 4.33506 8.43668 0.188493 0
12 298.098 61.1899 0.190289 0.345957 0.582294 0 0 1 1 35.7592 55.4213 4.08533 14.495 0 0 0 0 72 72 525.639 400.514 525 402.5 15.8517 10.0323 220 220 414.586 388.518 414 389 8.24825 8.34664 0 0 0 0 0.099668 0.699402 0 0 0 0 0 0 0 0 0 20.026 4.61747 2.28788 1.20766 0.161953 1 1 5.23143e-015 0.000264965 156 156 0 0 0 505.613 395.896 16.4965 3.07375 0 35.7592 55.4213 4.08533 14.495 0.161953 1
13 319.237 61.2715 -1.75446 0.142941 1.24984e-034 0 0 1 1 17052.5 300.145 181.064 22.2947 3 0 0 0 72 72 12214.7 416.292 11912 415.5 1054.9 12.6841 212 212 419.467 389.524 418 389 9.88003 8.66624 0 0 0 0 0.426003 0.699402 0 0 0 0 0 0 0 0 0 11709.1 20.3953 124.328 1.51495 0.421528 1 1 2.56454e-076 1.09797e-021 156 156 1 1 0 505.613 395.896 16.4965 3.07375 0 17052.5 300.145 181.064 22.2947 0.421528 1
14 340.564 62.2909 -2 0.161061 2.09621e-035 0 0 1 1 15429 95.0648 221.414 17.7959 6 0 0 0 70 70 10628.3 402.657 10219 403 1215.33 10.3866 205 205 420.22 390.156 420 390 9.86107 7.30532 0 0 0 0 0.35835 0.699402 0 0 0 0 0 0 0 0 0 10122.7 6.76073 145.266 1.26559 0.352732 1 1 1.06787e-065 9.62906e-007 156 156 1 0 0 505.613 395.896 16.4965 3.07375 0 15429 95.0648 221.414 17.7959 0.352732 1
15 362.115 61.1212 0 0.146303 1 39.6112 27.4353 1 1 39.6112 27.4353 5.27065 8.98298 5 1 0 1 64 64 488.125 398.688 486.5 398 14.0255 7.80695 219 219 419.831 389.676 419 390 9.83085 7.72758 0 0 0 0 0.0364585 0.699402 0 0 0 0 0 0 0 0 0 -17.4879 2.79108 2.19502 1.00642 0.131143 0 1 5.65003e-013 0.00708063 156 156 0 0 0 505.613 395.896 16.4965 3.07375 0 -41.9916 24.9123 5.27065 8.98298 0.131143 0
16 382.879 62.0364 0.187282 0.29187 0.521094 0 0 1 1 42.735 65.7757 3.67112 14.639 1 0 0 0 68 68 529.779 401.324 530.5 400 13.2077 9.7513 221 221 418.394 390.814 418 391 8.45005 9.11776 0 0 0 0 0.0594331 0.699402 0 0 0 0 0 0 0 0 0 24.1665 5.42711 2.07601 1.20786 0.135553 1 1 5.39846e-023 2.58458e-005 156 156 0 0 0 505.613 395.896 16.4965 3.07375 0 42.735 65.7757 3.67112 14.639 0.135553 1
17 403.911 61.8095 -1.78855 0.145517 1.01218e-034 0 0 1 1 17434.9 283.706 166.956 20.9529 2 1 0 0 69 69 12459.8 415.203 12178 413 950.814 11.6664 216 216 424.19 391.213 423 391.5 10.2828 8.37943 0 0 0 0 0.113956 0.699402 0 0 0 0 0 0 0 0 0 11954.2 19.3065 114.472 1.42587 0.113631 1 1 7.99984e-077 1.67493e-021 156 156 1 1 0 505.613 395.896 16.4965 3.07375 0 17434.9 283.706 166.956 20.9529 0.113631 1
18 425.793 63.0887 -1.96123 0.1587 4.4042e-035 0 0 1 1 16404.2 179.361 312.167 19.575 0 0 0 0 72 72 11519.4 408.361 10879 407 1778.38 11.3526 210 210 423.648 390.857 423 391 9.19796 8.59891 0 0 0 0 0.208042 0.699402 1 0 0 0 0 0 0 0 0 11013.8 12.4647 209.589 1.36036 0.205403 1 1 1.39532e-058 6.63154e-014 156 156 1 1 0 505.613 395.896 16.4965 3.07375 0 16404.2 179.361 312.167 19.575 0.205403 1
19 446.36 61.686 0 0.157767 1 39.6112 0 1 1 39.6112 28.184 5.37702 9.8621 0 0 0 0 74 74 505.108 399.054 502.5 401 15.556 9.26607 212 212 420.689 391.16 420 391 8.00872 8.82654 0 0 0 0 0.00233478 0.699402 0 0 0 0 0 0 0 0 0 -0.504784 3.15764 2.23932 1.10491 0.0937176 0 1 0.821958 0.00542455 156 156 0 0 0 505.613 395.896 16.4965 3.07375 0 -1.21208 28.184 5.37702 9.8621 0.0937176 0
20 467.023 61.9168 0.229028 0.215076 0.286936 0 0 1 1 55.8658 94.6615 3.57122 13.615 1 0 4 0 64 64 537.734 403.578 538.5 403.5 12.5777 8.61671 229 229 422.14 389.983 421 390 8.88215 8.46612 0 0 0 0 0.191837 0.699402 0 0 0 0 0 0 0 0 0 32.1215 7.68171 2.05337 1.10485 0.243401 1 1 1.64517e-033 1.55378e-009 156 156 0 0 0 505.613 395.896 16.4965 3.07375 0 55.8658 94.6615 3.57122 13.615 0.243401 1

Total number of rows: 22575

Table truncated, full table size 8801 Kbytes.




Supplementary data files not provided
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