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Sample GSM27934 Query DataSets for GSM27934
Status Public on Aug 20, 2004
Title Cy3 probe1 from young oocyte RNA2 vs Cy5 probe1 from aged oocyte RNA3
Sample type RNA
 
Channel 1
Source name Cy3 probe1 from young oocyte RNA2
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name Cy5 probe1 from aged oocyte RNA3
Organism Mus musculus
Extracted molecule total RNA
 
 
Description Cy3 probe1 from young oocyte RNA2 vs Cy5 probe1 from aged oocyte RNA3
 
Submission date Aug 05, 2004
Last update date May 27, 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)
GSE1646 Age-associated alteration of gene expression patterns in mouse oocytes

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 91.0599 66.6833 -0.182846 0.0318251 9.174e-009 0 0 1 1 310024 203493 2336.67 1338.92 1 1 0 0 74 74 14226.6 17893.4 13921 17703 891.119 989.854 196 196 401.74 406.495 400.5 405 10.0633 16.5559 0 0 0 0 0.912349 0.526224 0 0 0 0 0 0 1 1 0 13744.4 17488.5 103.592 115.068 0.912369 1 1 8.8204e-089 4.55851e-093 152 152 1 1 0 482.168 404.884 7.99723 3.27429 0 310024 203493 2336.67 1338.92 0.912369 1
2 112.52 66.207 -0.169585 0.0316712 8.57696e-008 0 0 1 1 530193 358797 6968.96 4712.79 2 3 0 0 72 72 23400.2 32030.6 22680 30988.5 2556.09 3524.81 193 193 401.876 407.995 401 406 10.106 17.1198 0 0 0 0 0.942556 0.526224 0 0 0 0 0 0 1 1 0 22918 31625.7 301.239 415.403 0.942558 1 1 8.68322e-070 8.27485e-070 152 152 1 1 0 482.168 404.884 7.99723 3.27429 0 530193 358797 6968.96 4712.79 0.942558 1
3 133.293 67.0677 0 0 1 0 0 1 1 -397.156 -8.00277 24.7183 15.4246 4 3 0 1 68 68 460.544 404.324 461 404.5 9.7237 8.62734 216 216 394.889 393.444 394 393 6.42138 9.62442 0 0 0 0 0.0222448 0.526224 0 0 0 0 0 0 0 0 0 -21.6235 -0.560028 1.34581 1.0794 0.0320285 0 0 1.52996e-030 0.60539 152 152 0 0 0 482.168 404.884 7.99723 3.27429 0 -397.156 -8.00277 24.7183 15.4246 0.0320285 0
4 155.352 66.5405 2 0 1 0 0 1 1 -57.6902 107.41 23.5845 16.1894 1 0 0 0 75 75 479.027 412.4 480 412 9.59726 9.53798 216 216 397.546 393.171 397 393 7.50613 9.4403 0 0 0 0 0.180725 0.526224 0 0 0 0 0 0 0 0 0 -3.141 7.51644 1.28408 1.13292 0.239501 0 1 0.0158195 3.15143e-009 152 152 0 0 0 482.168 404.884 7.99723 3.27429 0 -57.6902 107.41 23.5845 16.1894 0.239501 0
5 175.852 66.9655 -0.175422 0.0317376 3.25252e-008 0 0 1 1 317807 212198 1986.33 1199.33 0 3 0 0 68 68 14550.1 18669.4 14452.5 18335.5 725.039 851.253 218 218 402.528 400.78 403 399 8.74375 12.325 0 0 0 0 0.870692 0.526224 0 0 0 0 0 0 1 1 0 14068 18264.5 87.9263 103.23 0.870695 1 1 2.75344e-088 3.36072e-091 152 152 1 1 0 482.168 404.884 7.99723 3.27429 0 317807 212198 1986.33 1199.33 0.870695 1
6 196.914 66.6927 -0.167829 0.0316517 1.14305e-007 0 0 1 1 554246 376594 7226.63 4692.03 1 2 0 0 73 73 24388.9 33670 23810 32554 2663.26 3541.1 193 193 400.016 401.995 399 401 8.30692 14.2271 0 0 0 0 0.955597 0.526224 0 0 0 0 0 0 0 1 0 23906.8 33265.2 311.712 414.454 0.955597 1 1 8.79864e-071 3.46211e-072 152 152 1 1 0 482.168 404.884 7.99723 3.27429 0 554246 376594 7226.63 4692.03 0.955597 1
7 217.762 66.7219 2 0 1 0 0 1 1 -444.394 16.9463 22.9087 16.5408 3 0 0 0 72 72 457.972 406.069 457.5 406.5 9.03977 9.55978 232 232 394.095 392.539 394 392 6.91692 8.99486 0 0 0 0 -0.00454082 0.526224 0 0 0 0 0 0 0 0 0 -24.1954 1.18589 1.24729 1.15751 -0.0450007 0 0 1.48638e-039 0.308719 152 152 0 0 0 482.168 404.884 7.99723 3.27429 0 -444.394 16.9463 22.9087 16.5408 -0.0450007 0
8 239.404 67.1624 2 0 1 0 0 1 1 -3.84474 122.732 29.7985 14.6031 2 4 0 0 72 72 481.958 413.472 481 413.5 12.6184 8.37328 224 224 394.884 392.21 394.5 391 7.00832 9.63996 0 0 0 0 0.0536436 0.526224 0 0 0 0 0 0 0 0 0 -0.20933 8.58867 1.62241 1.02191 0.0675244 0 1 0.8976 1.15123e-012 152 152 0 1 0 482.168 404.884 7.99723 3.27429 0 -3.84474 122.732 29.7985 14.6031 0.0675244 0
9 260.357 67.1178 -0.180661 0.031799 1.33638e-008 0 0 1 1 321936 212377 1990.1 1132.38 0 2 0 0 73 73 14728.4 18690.6 14621 18600 752.413 833.017 216 216 396.426 397.69 396 397 7.98569 11.3994 0 0 0 0 0.882455 0.526224 0 0 0 0 0 0 0 1 0 14246.3 18285.7 88.0657 97.4976 0.882448 1 1 5.5546e-094 1.37573e-098 152 152 1 1 0 482.168 404.884 7.99723 3.27429 0 321936 212377 1990.1 1132.38 0.882448 1
10 281.637 67.0153 -0.157659 0.0315422 5.78244e-007 0 0 1 1 550817 383132 5943.19 4262.82 0 3 0 0 73 73 24235 34256.1 23653 33123 2189.72 3217.99 190 190 398.258 401.411 397 400.5 8.81328 13.3741 0 0 0 0 0.94351 0.526224 0 0 0 0 0 0 0 1 0 23752.9 33851.2 256.288 376.637 0.943509 1 1 1.21086e-076 1.08627e-075 152 152 1 1 0 482.168 404.884 7.99723 3.27429 0 550817 383132 5943.19 4262.82 0.943509 1
11 302.913 67.5 2 0 1 0 0 1 1 -427.38 48.883 28.276 16.4181 3 2 0 1 69 69 458.899 408.304 459 409 11.5976 9.28519 221 221 392.656 390.76 393 390 5.69524 8.93163 0 0 0 0 0.109405 0.526224 0 0 0 0 0 0 0 0 0 -23.2691 3.42079 1.53951 1.14892 0.0975257 0 1 2.10492e-027 0.00390183 152 152 0 0 0 482.168 404.884 7.99723 3.27429 0 -427.38 48.883 28.276 16.4181 0.0975257 0
12 323.889 67.2271 1.24867 0.531695 0.0188503 0 0 1 1 14.5058 257.167 17.5423 25.3242 4 0 1 0 68 68 483.206 418.574 482.5 419.5 8.86475 10.8989 226 226 392.978 391.752 393 392 6.54587 9.07992 0 0 0 0 -0.174414 0.526224 0 0 0 0 0 0 0 0 0 1.03822 13.69 1.25555 1.3481 -0.111949 0 1 0.409964 1.42934e-015 152 152 0 1 0 482.168 404.884 7.99723 3.27429 0 14.5058 257.167 17.5423 25.3242 -0.111949 0
13 345.087 67.7453 -0.180584 0.0317981 1.35422e-008 0 0 1 1 330597 218130 2001.88 1142.45 0 1 0 0 74 74 15093.8 19208.8 14985.5 19167.5 761.103 847.199 210 210 392.9 396.59 393 397 6.85283 10.3037 0 0 0 0 0.856191 0.526224 0 0 0 0 0 0 0 1 0 14611.7 18803.9 88.4788 98.4853 0.85617 1 1 1.0617e-095 2.77724e-100 152 152 1 1 0 482.168 404.884 7.99723 3.27429 0 330597 218130 2001.88 1142.45 0.85617 1
14 366.513 67.2171 -0.157429 0.0315398 5.99353e-007 0 0 1 1 557381 387903 6069.95 4237.28 2 3 0 0 72 72 24504.7 34696.7 23887.5 33686 2219.82 3178.49 200 200 392.245 397.265 392 396 6.753 10.7238 0 0 0 0 0.955274 0.526224 0 0 0 0 0 0 0 1 0 24022.6 34291.8 261.609 374.588 0.955271 1 1 1.56877e-075 1.94941e-075 152 152 1 1 0 482.168 404.884 7.99723 3.27429 0 557381 387903 6069.95 4237.28 0.955271 1
15 386.568 67.7153 2 0 1 0 0 1 1 -385.309 43.3752 24.2234 18.0706 1 0 0 0 74 74 461.189 407.919 460 408.5 9.87827 10.6356 215 215 387.758 390.73 387 391 5.97402 8.94906 0 0 0 0 0.0457833 0.526224 0 0 0 0 0 0 0 0 0 -20.9785 3.03536 1.31887 1.26457 0.0593606 0 0 1.93041e-031 0.0187092 152 152 0 0 0 482.168 404.884 7.99723 3.27429 0 -385.309 43.3752 24.2234 18.0706 0.0593606 0
16 408.559 67.6676 0.624669 0.210217 0.00296302 0 0 1 1 40.8057 171.945 17.3781 25.502 0 1 0 0 74 74 485.149 413.851 484.5 414 9.38767 11.2112 227 227 386.251 390.789 386 391 6.58931 9.42691 0 0 0 0 -0.300972 0.526224 0 0 0 0 0 0 0 0 0 2.98098 8.96779 1.26952 1.33005 -0.244853 0 1 0.0204247 2.29948e-009 152 152 0 1 0 482.168 404.884 7.99723 3.27429 0 40.8057 171.945 17.3781 25.502 -0.244853 0
17 429.848 68.1373 -0.172913 0.0317088 4.94819e-008 0 0 1 1 326473 219247 1699.19 1179.68 0 1 0 0 72 72 14914 19301.9 14803 19165.5 637.333 862.757 227 227 387.555 392.731 387 393 6.70625 8.97504 0 0 0 0 0.846479 0.526224 0 0 0 0 0 0 0 0 0 14431.9 18897 75.1133 101.677 0.846454 1 1 3.2893e-098 3.5577e-097 152 152 1 1 0 482.168 404.884 7.99723 3.27429 0 326473 219247 1699.19 1179.68 0.846454 1
18 450.878 67.8993 -0.152756 0.0314918 1.23049e-006 0 0 1 1 569847 400869 6156.5 4281.75 1 2 0 0 69 69 25011 35887.7 24614 34708 2201.28 3148.19 215 215 387.237 392.693 387 392 6.65537 9.00149 0 0 0 0 0.937092 0.526224 0 0 0 0 0 0 0 0 0 24528.9 35482.8 265.004 378.998 0.93709 1 1 2.86273e-073 1.32722e-073 152 152 1 1 0 482.168 404.884 7.99723 3.27429 0 569847 400869 6156.5 4281.75 0.93709 1
19 471.633 67.5462 2 0 1 0 0 1 1 -310.483 41.1494 27.3715 17.8077 0 0 0 0 76 76 465.263 407.763 464 406 11.6966 10.6143 234 234 386.457 389.628 387 389 5.68639 9.14562 0 0 0 0 0.0384196 0.526224 0 0 0 0 0 0 0 0 0 -16.9045 2.8796 1.49027 1.24617 0.0676051 0 0 2.81589e-020 0.0233515 152 152 0 0 0 482.168 404.884 7.99723 3.27429 0 -310.483 41.1494 27.3715 17.8077 0.0676051 0
20 493.216 67.8158 0.481897 0.121115 6.92512e-005 0 0 1 1 80.3237 243.636 20.0241 24.5286 3 3 0 0 70 70 488.229 417.186 487 416 11.4172 10.1214 224 224 385.875 389.813 386 390 6.15659 9.64577 0 0 0 0 -0.176957 0.526224 0 0 0 0 0 0 0 0 0 6.06091 12.3022 1.51094 1.23855 -0.109364 1 1 0.000115685 2.31058e-015 152 152 0 1 0 482.168 404.884 7.99723 3.27429 0 80.3237 243.636 20.0241 24.5286 -0.109364 0

Total number of rows: 22575

Table truncated, full table size 8819 Kbytes.




Supplementary data files not provided
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