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Sample GSM14702 Query DataSets for GSM14702
Status Public on Jan 09, 2004
Title 43h-Control replication 2
Sample type RNA
 
Channel 1
Source name 43h-Control, 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-Control 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 73.5446 59.851 -2 0.160202 9.10347e-036 0 0 1 1 215592 271.594 2343.12 13.8164 5 1 0 0 70 70 18092.8 430.2 17685.5 430 1607.22 10.6942 231 231 372.481 401.368 372 401 4.46029 8.44051 0 0 0 0 0.130084 0.494164 0 0 0 0 0 0 0 1 0 17675.3 25.6458 192.101 1.30464 0.127704 1 1 6.24837e-074 2.81248e-031 146 146 1 1 0 417.492 404.554 6.02684 3.15775 0 215592 271.594 2343.12 13.8164 0.127704 1
2 94.3312 58.5142 -2 0.160154 8.6869e-036 0 0 1 1 181396 174.323 2852.02 13.3225 1 0 0 0 75 75 14557.6 421.867 13989 420 1925.35 11.2326 227 227 372.308 400.286 372 400 4.72632 8.39574 0 0 0 0 0.0646114 0.494164 1 0 0 0 0 0 0 0 0 14140.1 17.3124 222.321 1.32309 0.0635573 1 1 2.4121e-066 1.39759e-021 146 146 1 1 0 417.492 404.554 6.02684 3.15775 0 181396 174.323 2852.02 13.3225 0.0635573 1
3 116.04 60.21 0 0.088022 1 90.1579 0 1 1 90.1579 61.8261 14.5892 8.41042 1 1 1 0 70 70 416.714 411.714 416 412 7.01167 7.85031 227 227 371.643 399.815 371 401 4.3243 8.16376 0 0 0 0 0.0171894 0.494164 0 0 0 0 0 0 0 0 0 -0.777236 7.16005 0.975255 0.974006 0.0820414 0 1 0.427058 1.49927e-010 146 146 0 0 0 417.492 404.554 6.02684 3.15775 0 -11.627 61.8261 14.5892 8.41042 0.0820414 0
4 137.381 59.4286 0 0.101503 1 81.1931 0 1 1 81.1931 60.508 14.0998 10.2734 1 2 0 0 74 74 421.189 410.865 422 411 7.91509 8.93864 221 221 372.118 400.172 372 400 4.11148 8.46637 0 0 0 0 0.019341 0.494164 0 0 0 0 0 0 0 0 0 3.69767 6.31063 1.04661 1.07146 0.0739316 1 1 0.000588946 8.11173e-008 146 146 0 0 0 417.492 404.554 6.02684 3.15775 0 49.8147 60.508 14.0998 10.2734 0.0739316 0
5 158.589 59.9265 -2 0.160189 8.98149e-036 0 0 1 1 223238 262.106 2435.11 13.1613 4 0 0 0 72 72 18718.6 429.306 18536.5 430 1693.92 10.3102 223 223 372.076 399.341 372 399 4.0122 8.23913 0 0 0 0 0.0861499 0.494164 0 0 0 0 0 0 0 0 0 18301.1 24.7513 199.631 1.24285 0.0844832 1 1 1.76247e-075 3.04849e-032 146 146 1 1 0 417.492 404.554 6.02684 3.15775 0 223238 262.106 2435.11 13.1613 0.0844832 1
6 179.722 59.1935 -2 0.160122 8.41635e-036 0 0 1 1 192828 146.575 3201.96 13.165 0 0 0 0 76 76 15319.9 419.237 14620 419 2157.28 11.2687 220 220 372.341 398.923 372 398 3.96067 7.09096 0 0 0 0 0.155312 0.494164 1 0 0 0 0 0 0 0 0 14902.4 14.6826 247.458 1.31876 0.152429 1 1 2.92881e-065 5.12888e-018 146 146 1 1 0 417.492 404.554 6.02684 3.15775 0 192828 146.575 3201.96 13.165 0.152429 1
7 201.725 60.2941 0 0.0947731 1 90.1579 0 1 1 90.1579 60.3356 14.6247 9.91275 2 0 1 0 72 72 414.833 411.542 414.5 411 7.13452 9.48526 220 220 371.895 398.609 372 398 4.29112 8.16451 0 0 0 0 0.0587958 0.494164 0 0 0 0 0 0 0 0 0 -2.65819 6.98743 0.977625 1.14799 0.106635 0 1 0.00749971 3.92841e-008 146 146 0 0 0 417.492 404.554 6.02684 3.15775 0 -39.7649 60.3356 14.6247 9.91275 0.106635 0
8 222.118 59.8824 0 0.0963534 1 80.7716 0 1 1 80.7716 65.9532 13.9511 9.64829 0 2 0 1 68 68 422.353 411.397 421 410.5 7.53453 7.96848 213 213 371.333 398.437 372 398 4.29421 7.76433 0 0 0 0 -0.0259856 0.494164 0 0 0 0 0 0 0 0 0 4.86142 6.84282 1.04097 1.00104 0.039798 1 1 8.67935e-006 1.70113e-009 146 146 0 0 0 417.492 404.554 6.02684 3.15775 0 65.1526 65.9532 13.9511 9.64829 0.039798 0
9 243.553 60.7377 -2 0.160156 8.69919e-036 0 0 1 1 230220 223.573 2784.28 12.4385 2 2 0 0 73 73 19093.2 425.89 18716 426 1929.77 9.89327 218 218 371.697 399.367 372 400 4.35203 8.58426 0 0 0 0 -0.0313614 0.494164 0 0 0 0 0 0 0 0 0 18675.7 21.3362 225.863 1.18704 -0.0303516 1 1 4.15523e-073 1.01955e-029 146 146 1 1 0 417.492 404.554 6.02684 3.15775 0 230220 223.573 2784.28 12.4385 -0.0303516 1
10 263.984 59.6505 -2 0.160154 8.68626e-036 0 0 1 1 192654 185.117 3130.5 12.2892 0 0 0 0 76 76 15580 422.763 14860 422.5 2147.89 10.289 219 219 372.205 398.128 372 398 4.22843 7.57725 0 0 0 0 0.102611 0.494164 1 0 0 0 0 0 0 0 0 15162.5 18.2089 246.38 1.20881 0.1004 1 1 5.95255e-066 2.16762e-025 146 146 1 1 0 417.492 404.554 6.02684 3.15775 0 192654 185.117 3130.5 12.2892 0.1004 1
11 285.5 60.902 0 0.124986 1 90.1579 0 1 1 90.1579 39.2054 14.6814 9.99048 0 0 0 0 74 74 415.892 409.095 414 410 7.27082 9.6956 216 216 372.523 399.796 372 399 4.5586 8.19842 0 0 0 0 0.0563057 0.494164 0 0 0 0 0 0 0 0 0 -1.59963 4.54036 0.981416 1.15699 0.103967 0 1 0.105634 0.000181628 146 146 0 0 0 417.492 404.554 6.02684 3.15775 0 -23.9295 39.2054 14.6814 9.99048 0.103967 0
12 306.914 60.4286 0 0.11628 1 80.7401 0 1 1 80.7401 58.5022 14.1679 11.0247 1 0 0 0 74 74 423.122 410.622 423.5 410.5 8.02215 9.57551 221 221 372.149 398.955 372 398 4.2832 8.05536 0 0 0 0 -0.156858 0.494164 0 0 0 0 0 0 0 0 0 5.6301 6.06738 1.05757 1.1434 -0.0813854 1 1 5.0401e-007 9.49693e-007 146 146 0 0 0 417.492 404.554 6.02684 3.15775 0 75.425 58.5022 14.1679 11.0247 -0.0813854 0
13 327.814 60.7314 -2 0.160211 9.18179e-036 0 0 1 1 228473 300.321 2571.28 17.9024 2 2 0 0 71 71 19392 432.549 19058 431 1799.34 13.8881 213 213 372.498 398.953 372 399 4.42615 8.41874 0 0 0 0 0.0715091 0.494164 0 0 0 0 0 0 0 0 0 18974.5 27.9951 213.543 1.66881 0.0708074 1 1 1.03598e-073 7.55017e-027 146 146 1 1 0 417.492 404.554 6.02684 3.15775 0 228473 300.321 2571.28 17.9024 0.0708074 1
14 348.076 61.0137 -2 0.160167 8.79381e-036 0 0 1 1 189884 197.301 2931.42 14.8427 0 0 0 0 69 69 15422 423.884 15164 425 1924.13 11.8824 217 217 372.954 399.465 373 399 4.51004 7.85222 0 0 0 0 -0.043998 0.494164 1 0 0 0 0 0 0 0 0 15004.5 19.3298 231.638 1.45415 -0.0430903 1 1 7.56841e-063 3.94492e-021 146 146 1 1 0 417.492 404.554 6.02684 3.15775 0 189884 197.301 2931.42 14.8427 -0.0430903 1
15 369.868 61.1887 0 0.119687 1 85.1038 0 1 1 85.1038 41.1766 14.8874 10.6253 1 0 0 0 72 72 417.653 409.056 417 410 7.88144 9.60324 230 230 372.5 399.017 373 399 4.67526 7.91327 0 0 0 0 0.212771 0.494164 0 0 0 0 0 0 0 0 0 0.161256 4.50132 1.05429 1.16153 0.235248 0 1 0.878708 0.000219248 146 146 0 0 0 417.492 404.554 6.02684 3.15775 0 2.27706 41.1766 14.8874 10.6253 0.235248 0
16 391.406 60.1981 0.110278 0.175446 0.529639 80.1726 0 1 1 80.1726 103.348 13.0938 12.5974 0 0 0 0 76 76 422.684 415.197 423 414 7.39768 11.0779 225 225 372.027 399.16 372 399 4.32489 8.02681 0 0 0 0 0.0375406 0.494164 0 0 0 0 0 0 0 0 0 5.19269 10.6431 0.984307 1.29732 0.0821442 1 1 5.48899e-007 2.88442e-012 146 146 0 1 0 417.492 404.554 6.02684 3.15775 0 69.0761 103.348 13.0938 12.5974 0.0821442 1
17 412.303 61.6645 -2 0.160181 8.91625e-036 0 0 1 1 239230 269.852 3331.64 14.2216 0 2 0 0 72 72 20187.6 429.833 19491.5 430 2336.24 11.0848 219 219 372.402 398.717 373 398 4.51737 8.87023 0 0 0 0 0.110442 0.494164 0 0 0 0 0 0 0 0 0 19770.1 25.2791 275.329 1.33224 0.108472 1 1 4.99981e-068 1.04894e-030 146 146 1 1 0 417.492 404.554 6.02684 3.15775 0 239230 269.852 3331.64 14.2216 0.108472 1
18 433.596 60.6095 -2 0.160138 8.54698e-036 0 0 1 1 201049 172.559 3329.57 14.0644 0 0 0 0 76 76 16205.4 421.566 15520.5 422 2279.38 11.8708 229 229 372.939 398.646 372 398 4.60603 7.78673 0 0 0 0 -0.195353 0.494164 1 0 0 0 0 0 0 0 0 15787.9 17.0116 261.464 1.38652 -0.191674 1 1 2.40756e-065 3.99983e-020 146 146 1 1 0 417.492 404.554 6.02684 3.15775 0 201049 172.559 3329.57 14.0644 -0.191674 1
19 455.079 61.8416 0 0.112736 1 82.85 0 1 1 82.85 55.1416 14.8529 9.74618 0 1 0 0 71 71 418.437 410.423 418 410 8.07595 8.45773 227 227 372.282 399.498 372 399 4.62293 7.98083 0 0 0 0 -0.140568 0.494164 0 0 0 0 0 0 0 0 0 0.945098 5.8683 1.08046 1.03721 -0.0631913 0 1 0.383647 2.32405e-007 146 146 0 0 0 417.492 404.554 6.02684 3.15775 0 12.9921 55.1416 14.8529 9.74618 -0.0631913 0
20 476.4 60.9975 0.116599 0.167351 0.485969 0 0 1 1 83.7916 109.597 14.8686 11.6838 0 1 0 0 75 75 423.813 415.8 423 415 8.70181 10.1329 223 223 372.018 399.538 372 399 4.38668 7.89213 0 0 0 0 0.0682308 0.494164 0 0 0 0 0 0 0 0 0 6.32181 11.2458 1.12179 1.19888 0.107542 1 1 1.32953e-007 1.33831e-014 146 146 0 1 0 417.492 404.554 6.02684 3.15775 0 83.7916 109.597 14.8686 11.6838 0.107542 1

Total number of rows: 22575

Table truncated, full table size 8814 Kbytes.




Supplementary data files not provided
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