NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM27933 Query DataSets for GSM27933
Status Public on Aug 20, 2004
Title Cy3 probe1 from aged oocyte RNA3 vs Cy5 probe1 from young oocyte RNA2
Sample type RNA
 
Channel 1
Source name Cy3 probe1 from aged oocyte RNA3
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name Cy5 probe1 from young oocyte RNA2
Organism Mus musculus
Extracted molecule total RNA
 
 
Description Cy3 probe1 from aged oocyte RNA3 vs Cy5 probe1 from young oocyte RNA2
 
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 84.1306 69.8694 0.166692 0.0316391 1.37509e-007 0 0 1 1 495390 727175 4046.88 6477.53 3 3 0 0 70 70 35916 46035.6 35426.5 45107 2421.55 3400.71 207 207 391.188 400.531 391 398 7.25729 12.3814 0 0 0 0 0.980894 0.825182 0 0 0 0 0 0 0 0 0 35430 45629.9 289.431 406.462 0.980893 1 1 1.96233e-082 7.49341e-080 158 158 1 1 0 486.05 405.695 7.53822 3.88771 0 495390 727175 4046.88 6477.53 0.980893 1
2 105.508 69.7514 0.168273 0.0316566 1.06315e-007 0 0 1 1 721314 1.06267e+006 9696.19 109.379 0 0 1 14 62 62 53333.2 65498.9 51754.5 65517 5593.63 52.6992 211 211 391.839 404.668 392 403 6.95171 13.6097 0 54 0 1 0.368274 0.825182 0 0 0 0 0 0 0 0 0 52847.2 65093.2 710.392 6.69995 0.367903 1 1 1.4261e-061 2.97665e-191 158 158 1 1 0 486.05 405.695 7.53822 3.88771 0 721314 1.06267e+006 9696.19 109.379 0.367903 1
3 126.94 69.7143 2 0 1 0 0 1 1 -254.649 62.8925 18.7664 18.7856 2 0 0 0 73 73 467.973 409.671 469 411 10.1639 9.79662 210 210 390.481 393.857 390 394 6.39842 9.38178 0 0 0 0 0.139394 0.825182 0 0 0 0 0 0 0 0 0 -18.0773 3.97595 1.33221 1.18759 0.114462 0 1 3.07254e-025 0.00122763 158 158 0 0 0 486.05 405.695 7.53822 3.88771 0 -254.649 62.8925 18.7664 18.7856 0.114462 0
4 147.856 70.0075 0.447509 0.243923 0.0665604 0 0 1 1 38.4115 107.639 18.7994 22.6904 0 0 0 0 70 70 489.2 411.586 489 412 11.883 10.0614 226 226 389.447 393.642 388 393 6.18452 9.74337 0 0 0 0 -0.203307 0.825182 0 0 0 0 0 0 0 0 0 3.15007 5.89043 1.54171 1.2417 -0.152588 0 1 0.0438148 9.26608e-006 158 158 0 0 0 486.05 405.695 7.53822 3.88771 0 38.4115 107.639 18.7994 22.6904 -0.152588 0
5 169.163 70.0008 0.164124 0.031611 2.08073e-007 0 0 1 1 512577 747968 4398.13 6523.23 2 3 0 0 69 69 37218.6 47246.7 36491 46440 2618.08 3393.37 224 224 391.661 399.509 391.5 399 7.01575 10.6033 0 0 0 0 0.985306 0.825182 0 0 0 0 0 0 0 0 0 36732.5 46841 315.18 408.513 0.985305 1 1 4.95268e-080 1.49159e-079 158 158 1 1 0 486.05 405.695 7.53822 3.88771 0 512577 747968 4398.13 6523.23 0.985305 1
6 190.072 70.0134 0.167044 0.031643 1.29877e-007 0 0 1 1 723650 1.0631e+006 8259.6 5.22912 0 0 0 2 67 67 53510.5 65517.6 52249 65518 4953.86 0.680543 202 202 393.713 401.109 394 400 6.81648 11.443 0 67 0 1 0.141443 0.825182 0 0 0 0 0 0 0 0 0 53024.5 65111.9 605.211 0.32027 0.037399 1 1 5.0682e-070 0 158 158 1 1 0 486.05 405.695 7.53822 3.88771 0 723650 1.0631e+006 8259.6 5.22912 0.037399 1
7 211.692 69.9538 0 0 1 0 0 1 1 -332.96 -9.94356 19.4697 18.8024 1 0 0 0 75 75 462.413 405.067 463 404 10.7842 9.93946 207 207 391.498 392.72 392 393 6.227 8.28783 0 0 0 0 -0.125071 0.825182 0 0 0 0 0 0 0 0 0 -23.6366 -0.628614 1.38214 1.18865 -0.093564 0 0 1.05702e-032 0.598292 158 158 0 0 0 486.05 405.695 7.53822 3.88771 0 -332.96 -9.94356 19.4697 18.8024 -0.093564 0
8 232.575 69.5337 0.224116 0.245563 0.361421 0 0 1 1 48.1966 80.7481 18.3298 22.6297 0 0 0 0 77 77 490 410.117 492 410 12.0863 10.5294 221 221 391.602 393.842 391 394 7.26353 9.84781 0 0 0 0 0.19138 0.825182 0 0 0 0 0 0 0 0 0 3.95007 4.4216 1.50226 1.23915 0.19146 1 1 0.00982855 0.000589752 158 158 0 0 0 486.05 405.695 7.53822 3.88771 0 48.1966 80.7481 18.3298 22.6297 0.19146 1
9 253.835 70.0966 0.173038 0.0317102 4.84672e-008 0 0 1 1 521641 776979 4796.62 7284.87 1 2 0 0 70 70 37934.7 48977 37202.5 48070.5 2881.03 3810.14 221 221 396.226 398.353 395 397 6.65538 11.0442 0 0 0 0 0.980539 0.825182 0 0 0 0 0 0 0 0 0 37448.6 48571.3 344.349 455.399 0.980537 1 1 6.61913e-079 2.51605e-078 158 158 1 1 0 486.05 405.695 7.53822 3.88771 0 521641 776979 4796.62 7284.87 0.980537 1
10 274.965 70.2008 0.156541 0.0315306 6.87964e-007 0 0 1 1 741969 1.06396e+006 8823.05 5.35454 0 0 1 3 70 70 54897.5 65517.2 53677 65518 5413.42 0.905584 216 216 397.231 402.282 397 402 7.55274 13.565 1 70 0 1 -0.0149368 0.825182 0 0 0 0 0 0 0 0 0 54411.5 65111.5 647.028 0.327682 -0.00432 1 1 2.94291e-071 0 158 158 1 1 0 486.05 405.695 7.53822 3.88771 0 741969 1.06396e+006 8823.05 5.35454 -0.00432 1
11 296.5 70 2 0 1 0 0 1 1 -320.392 40.6308 17.9233 19.3973 1 1 0 0 72 72 463.306 408.264 464 407 9.52186 10.0688 221 221 391.036 393.629 391 392 6.48064 8.51138 0 0 0 0 -0.0668143 0.825182 0 0 0 0 0 0 0 0 0 -22.7444 2.56861 1.27236 1.22626 -0.0314667 0 0 9.53417e-035 0.0393334 158 158 0 0 0 486.05 405.695 7.53822 3.88771 0 -320.392 40.6308 17.9233 19.3973 -0.0314667 0
12 317.279 70.2513 0.552132 0.284907 0.052631 0 0 1 1 26.971 96.1675 14.6657 24.859 3 0 0 0 72 72 488.25 410.986 487 410 8.78339 11.3044 216 216 391.88 393.486 392 394 6.12538 8.78317 0 0 0 0 0.056776 0.825182 0 0 0 0 0 0 0 0 0 2.20007 5.29083 1.19631 1.36766 0.0438174 0 1 0.0683693 0.000224273 158 158 0 0 0 486.05 405.695 7.53822 3.88771 0 26.971 96.1675 14.6657 24.859 0.0438174 1
13 338.358 70.1807 0.174983 0.0317325 3.50124e-008 0 0 1 1 523567 783350 4973.74 7012.61 2 2 0 0 75 75 38087.3 49356.7 37606 48393 3093.45 3795.03 214 214 395.14 398.248 395 397 7.02103 11.0861 0 0 0 0 0.937383 0.825182 0 0 0 0 0 0 0 0 0 37601.2 48951 357.201 438.213 0.937381 1 1 2.35571e-082 2.99196e-084 158 158 1 1 0 486.05 405.695 7.53822 3.88771 0 523567 783350 4973.74 7012.61 0.937381 1
14 359.406 70.5742 0.153183 0.0314961 1.15298e-006 0 0 1 1 747925 1.06424e+006 8723.77 5.30602 0 0 0 1 76 76 55348.6 65517.2 53424 65517 5578.65 0.85962 206 206 395.937 402.044 395.5 400.5 7.95971 11.2866 1 76 0 1 -0.153754 0.825182 0 0 0 0 0 0 0 0 0 54862.6 65111.5 639.915 0.324628 -0.0461463 1 1 1.34257e-076 0 158 158 1 1 0 486.05 405.695 7.53822 3.88771 0 747925 1.06424e+006 8723.77 5.30602 -0.0461463 1
15 381 70.5 2 0 1 0 0 1 1 -372.993 21.3163 21.8927 17.9462 3 3 0 0 70 70 459.571 407.043 459 408 11.9959 9.13258 230 230 392.526 394.943 392 396 6.7018 9.25719 0 0 0 0 0.125978 0.825182 0 0 0 0 0 0 0 0 0 -26.4785 1.34758 1.55415 1.13452 0.124873 0 0 1.71429e-030 0.238418 158 158 0 0 0 486.05 405.695 7.53822 3.88771 0 -372.993 21.3163 21.8927 17.9462 0.124873 0
16 403.175 69.9649 0.605216 0.205876 0.00328514 0 0 1 1 35.0293 141.139 15.3269 25.5753 2 0 1 0 69 69 488.928 413.406 489 413 9.1961 11.318 222 222 392.459 392.874 392 393 7.32229 9.26055 0 0 0 0 0.0397071 0.825182 0 0 0 0 0 0 0 0 0 2.8776 7.71052 1.25908 1.39719 0.0553226 0 1 0.0242069 4.65922e-007 158 158 0 0 0 486.05 405.695 7.53822 3.88771 0 35.0293 141.139 15.3269 25.5753 0.0553226 1
17 423.131 70.7588 0.180474 0.0317967 1.37984e-008 0 0 1 1 526443 797674 4377.45 6524.12 1 1 0 0 72 72 38322.3 50214.1 37743 49429.5 2669.59 3456.73 199 199 395.749 399.558 396 399 8.01685 10.2003 0 0 0 0 0.98168 0.825182 0 0 0 0 0 0 0 0 0 37836.3 49808.4 314.614 407.38 0.981679 1 1 8.51637e-084 2.65341e-084 158 158 1 1 0 486.05 405.695 7.53822 3.88771 0 526443 797674 4377.45 6524.12 0.981679 1
18 444.456 70.8504 0.14625 0.0314272 3.26169e-006 0 0 1 1 760378 1.06483e+006 8635.47 5.19079 0 0 0 4 72 72 56292.4 65517.7 54449.5 65518 5377.82 0.605142 209 209 395.646 401.086 396 400 6.83803 12.7537 3 72 0 1 0.0661896 0.825182 0 0 0 0 0 0 0 0 0 55806.4 65112 633.782 0.317406 0.0154904 1 1 3.01263e-074 0 158 158 1 1 0 486.05 405.695 7.53822 3.88771 0 760378 1.06483e+006 8635.47 5.19079 0.0154904 1
19 465.941 70.8074 2 0 1 0 0 1 1 -304.572 34.8747 18.1861 21.2667 1 1 1 0 70 70 464.429 407.9 464 407.5 9.56529 10.9467 219 219 392.968 395.658 393 395 6.55631 9.18797 0 0 0 0 -0.0280973 0.825182 0 0 0 0 0 0 0 0 0 -21.6214 2.20472 1.29101 1.34444 0.0152876 0 0 7.262e-032 0.10512 158 158 0 0 0 486.05 405.695 7.53822 3.88771 0 -304.572 34.8747 18.1861 21.2667 0.0152876 0
20 486.378 70.7816 0.176465 0.150161 0.239928 0 0 1 1 84.8001 127.31 19.0655 26.9089 1 0 0 0 75 75 493.053 412.613 495 412 12.6083 12.3768 215 215 393.298 395.586 393 395 6.57983 9.1156 0 0 0 0 -0.124652 0.825182 0 0 0 0 0 0 0 0 0 7.0034 6.91805 1.57456 1.46224 -0.0996426 1 1 2.25494e-005 9.32493e-006 158 158 0 0 0 486.05 405.695 7.53822 3.88771 0 84.8001 127.31 19.0655 26.9089 -0.0996426 1

Total number of rows: 22575

Table truncated, full table size 8789 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap