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Sample GSM27936 Query DataSets for GSM27936
Status Public on Aug 20, 2004
Title Cy3 probe1 from young oocyte RNA5 vs Cy5 probe1 from aged oocyte RNA2
Sample type RNA
 
Channel 1
Source name Cy3 probe1 from young oocyte RNA5
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name Cy5 probe1 from aged oocyte RNA2
Organism Mus musculus
Extracted molecule total RNA
 
 
Description Cy3 probe1 from young oocyte RNA5 vs Cy5 probe1 from aged 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 75.3454 59.0823 0.00505461 0.0307102 0.869266 0 0 1 1 342113 346118 3406.59 3630.62 5 5 0 0 71 71 24861.1 28545 24963 28359 2044.37 2487.05 218 218 374.445 385.661 374 385 5.76732 9.0102 0 0 0 0 0.963867 0.665496 0 0 0 0 0 0 0 0 0 24366 28138.4 242.624 295.159 0.963862 1 1 2.0983e-077 7.83467e-076 155 155 1 1 0 495.073 406.604 9.37457 4.49386 0 342113 346118 3406.59 3630.62 0.963862 1
2 96.5989 58 0.0202146 0.0307231 0.510564 0 0 1 1 614484 643762 8220.15 8119.35 3 0 0 0 73 73 43898.9 53177.7 42536 51083 4960.87 5686.61 215 215 374.256 387.247 374 387 5.08476 10.5998 0 0 0 0 0.956153 0.665496 0 0 0 0 0 1 0 0 0 43403.8 52771.1 580.627 665.568 0.956152 1 1 5.45346e-070 8.26777e-072 155 155 1 1 0 495.073 406.604 9.37457 4.49386 0 614484 643762 8220.15 8119.35 0.956152 1
3 117.06 59.5448 2 0 1 0 0 1 1 -24.5674 106.85 21.0305 18.2624 0 0 0 0 75 75 493.147 414.493 491 415 12.7063 11.2519 220 220 372.459 382.355 372 382 4.8317 8.95762 0 0 0 0 -0.101082 0.665496 0 0 0 0 0 0 0 0 0 -1.92649 7.88959 1.64914 1.34846 -0.0863546 0 1 0.245166 8.74223e-008 155 155 0 0 0 495.073 406.604 9.37457 4.49386 0 -24.5674 106.85 21.0305 18.2624 -0.0863546 0
4 138.85 58.3848 0.105856 0.0780058 0.174774 0 0 1 1 189.525 241.836 19.5477 20.8433 4 1 0 0 71 71 511.761 422.507 512 421 13.0411 11.1418 216 216 373.847 381.537 374 381 5.52287 8.15994 0 0 0 0 0.0191346 0.665496 0 0 0 0 0 0 0 0 0 16.6874 15.9033 1.72115 1.37067 0.0223066 1 1 3.11465e-016 7.16029e-019 155 155 0 1 0 495.073 406.604 9.37457 4.49386 0 189.525 241.836 19.5477 20.8433 0.0223066 1
5 159.528 59.6872 0.0178637 0.0307201 0.560904 0 0 1 1 366194 381571 3280.61 3369.6 5 5 0 0 71 71 26546.3 31462.7 26125 30939 1966.52 2310.89 213 213 374.667 383.394 375 383 5.29121 9.47212 0 0 0 0 0.492748 0.665496 0 0 0 0 0 0 0 0 0 26051.2 31056.1 233.384 274.252 0.492746 1 1 1.34266e-080 4.95039e-081 155 155 1 1 0 495.073 406.604 9.37457 4.49386 0 366194 381571 3280.61 3369.6 0.492746 1
6 181.255 58.4977 0.0484895 0.0307889 0.115279 0 0 1 1 595340 665663 7242.75 7687.16 3 0 0 0 73 73 42546.1 54973.7 40887 53368 4370.96 5383.98 220 220 377 385.873 377 385.5 5.09812 11.0578 0 0 0 0 0.979757 0.665496 0 0 0 0 0 1 0 0 0 42051.1 54567.1 511.582 630.148 0.979756 1 1 6.33835e-073 1.54579e-074 155 155 1 1 0 495.073 406.604 9.37457 4.49386 0 595340 665663 7242.75 7687.16 0.979756 1
7 202.059 59.6951 2 0 1 0 0 1 1 -102.028 112.534 17.4792 16.9099 5 2 0 1 69 69 487.072 414.913 487 415 9.51364 9.92877 217 217 375.295 380.696 375 380 5.34076 8.36547 0 0 0 0 -0.14363 0.665496 0 0 0 0 0 0 0 0 0 -8.00069 8.3093 1.37066 1.2486 -0.0783371 0 1 4.06886e-008 3.14491e-009 155 155 0 0 0 495.073 406.604 9.37457 4.49386 0 -102.028 112.534 17.4792 16.9099 -0.0783371 0
8 223.849 58.9823 0.0987271 0.0814898 0.225693 0 0 1 1 181.499 227.825 19.4648 20.5744 1 4 0 0 67 67 511.09 421.552 511 423 12.6368 10.6476 220 220 375.891 381.027 375 380 5.90928 8.19228 0 0 0 0 0.0969193 0.665496 0 0 0 0 0 0 0 0 0 16.0164 14.9485 1.71767 1.34997 0.0991418 1 1 3.32705e-015 1.51471e-017 155 155 0 1 0 495.073 406.604 9.37457 4.49386 0 181.499 227.825 19.4648 20.5744 0.0991418 1
9 244.443 60.2283 -0.000678111 0.0307093 0.982383 0 0 1 1 407978 407341 3623.13 3891.85 2 4 0 0 71 71 29484 33599.9 28921 33115 2169.24 2672.25 219 219 377.082 383.584 377 383 5.6595 8.24153 0 0 0 0 0.985663 0.665496 0 0 0 0 0 0 0 0 0 28988.9 33193.3 257.442 317.138 0.985659 1 1 7.31046e-081 1.18706e-078 155 155 1 1 0 495.073 406.604 9.37457 4.49386 0 407978 407341 3623.13 3891.85 0.985659 1
10 266.057 58.9844 0.0530136 0.0308045 0.0852562 0 0 1 1 625367 706560 7404.24 7000.46 2 0 0 0 67 67 44634.6 58368.8 43072 56868 4277.69 4700.67 204 204 377.779 388.436 378 389 5.94601 9.52522 0 6 0 0 0.945106 0.665496 0 0 0 0 0 1 0 0 0 44139.5 57962.2 522.604 574.278 0.945105 1 1 5.57173e-069 4.77254e-074 155 155 1 1 0 495.073 406.604 9.37457 4.49386 0 625367 706560 7404.24 7000.46 0.945105 1
11 286.923 60.3991 2 0 1 0 0 1 1 -128.457 102.648 16.7964 16.1599 2 1 2 0 71 71 485 414.183 485 413 9.10573 9.58318 216 216 375.782 384.014 376 384 5.04435 7.93197 0 0 0 0 0.282237 0.665496 0 0 0 0 0 0 0 0 0 -10.0732 7.57936 1.31711 1.19322 0.231308 0 1 3.01631e-012 1.02633e-008 155 155 0 0 0 495.073 406.604 9.37457 4.49386 0 -128.457 102.648 16.7964 16.1599 0.231308 0
12 308.251 59.6445 0.0176169 0.0802945 0.826336 0 0 1 1 202.806 211.202 18.8923 20.0758 0 4 0 1 70 70 512.957 420.471 512 421 12.4335 10.6072 228 228 376.715 384.987 377 385 5.16787 8.23364 0 0 0 0 0.0269683 0.665496 0 0 0 0 0 0 0 0 0 17.884 13.8677 1.66597 1.31819 0.0415941 1 1 1.25033e-018 8.90143e-017 155 155 0 1 0 495.073 406.604 9.37457 4.49386 0 202.806 211.202 18.8923 20.0758 0.0415941 1
13 329.532 60.8916 0.0136795 0.0307156 0.65606 0 0 1 1 396804 409501 2834.39 3341.28 6 6 0 0 69 69 28694.4 33770.8 28596 33267 1673.19 2261.32 223 223 378.099 386.852 378 387 5.43505 8.63215 0 0 0 0 0.960182 0.665496 0 0 0 0 0 0 0 0 0 28199.3 33364.1 201.43 272.231 0.960175 1 1 2.00071e-085 1.64495e-081 155 155 1 1 0 495.073 406.604 9.37457 4.49386 0 396804 409501 2834.39 3341.28 0.960175 1
14 351.123 59.7238 0.0597046 0.03083 0.052797 0 0 1 1 623424 715300 6972.49 6532.34 2 0 0 0 73 73 44494.7 59089.5 43557 59029 4204.5 4578.82 210 210 378.486 389.586 378 389 5.93363 9.55542 0 7 0 0 0.939531 0.665496 0 0 0 0 0 1 0 0 0 43999.6 58682.9 492.1 535.91 0.93953 1 1 1.57288e-075 8.038e-082 155 155 1 1 0 495.073 406.604 9.37457 4.49386 0 623424 715300 6972.49 6532.34 0.93953 1
15 372.382 61.127 2 0 1 0 0 1 1 -139.57 96.2991 17.7906 16.4911 0 3 0 2 70 70 484.129 413.714 484 412.5 9.82591 9.72989 216 216 375.995 384.491 376 384 5.16563 8.74975 0 0 0 0 0.178963 0.665496 0 0 0 0 0 0 0 0 0 -10.9446 7.11055 1.39508 1.21767 0.153591 0 1 1.50333e-012 9.97952e-008 155 155 0 0 0 495.073 406.604 9.37457 4.49386 0 -139.57 96.2991 17.7906 16.4911 0.153591 0
16 393.047 60.0988 0.110161 0.0960811 0.251573 0 0 1 1 148.395 191.241 19.2334 19.7923 1 2 1 0 65 65 508.231 419.092 507 421 12.3361 10.0058 218 218 376.569 384.225 376 384 6.03655 8.17211 0 0 0 0 -0.11423 0.665496 0 0 0 0 0 0 0 0 0 13.1576 12.4886 1.70535 1.29249 -0.0900762 1 1 1.10768e-011 8.19847e-015 155 155 0 1 0 495.073 406.604 9.37457 4.49386 0 148.395 191.241 19.2334 19.7923 -0.0900762 1
17 413.794 60.9573 0.0178494 0.0307201 0.561218 0 0 1 1 413498 430847 3214.42 3725.92 0 2 0 0 71 71 29862.2 35532.2 29457 35092 1923.61 2559.55 230 230 379.213 388.526 378.5 389 6.71782 8.47945 0 0 0 0 0.981739 0.665496 0 0 0 0 0 0 0 0 0 29367.1 35125.6 228.292 303.763 0.981734 1 1 6.84844e-085 1.15241e-081 155 155 1 1 0 495.073 406.604 9.37457 4.49386 0 413498 430847 3214.42 3725.92 0.981734 1
18 435.439 60.302 0.0625491 0.0308417 0.0425532 0 0 1 1 637228 735943 6299.13 5144.55 5 0 0 0 71 71 45453.6 60803.5 44219 60582 3744.78 3557.52 213 213 381.146 392.667 380 392 6.84894 10.9392 0 9 0 0 0.839736 0.665496 0 0 0 0 0 1 0 0 0 44958.5 60396.9 444.425 422.2 0.839736 1 1 1.26691e-077 4.17068e-088 155 155 1 1 0 495.073 406.604 9.37457 4.49386 0 637228 735943 6299.13 5144.55 0.839736 1
19 456.06 61.4549 2 0 1 0 0 1 1 -141.554 132.196 19.1729 20.0069 1 0 0 0 74 74 483.973 416.365 484.5 415 11.1944 12.3228 213 213 378.075 385.455 378 385 5.44821 8.44483 0 0 0 0 -0.0548427 0.665496 0 0 0 0 0 0 0 0 0 -11.1002 9.76113 1.50347 1.47727 -0.0462943 0 1 1.9964e-011 3.59787e-009 155 155 0 0 0 495.073 406.604 9.37457 4.49386 0 -141.554 132.196 19.1729 20.0069 -0.0462943 0
20 477.798 60.155 0.0640723 0.0766093 0.402957 0 0 1 1 203.209 235.513 18.4784 21.0755 0 0 0 0 74 74 512.946 422.108 513 421.5 12.3897 11.5243 208 208 377.851 383.404 378 383 5.05256 8.07575 0 0 0 0 0.0861001 0.665496 0 0 0 0 0 0 0 0 0 17.8728 15.5044 1.62523 1.38745 0.0929906 1 1 1.25406e-019 2.79995e-018 155 155 0 1 0 495.073 406.604 9.37457 4.49386 0 203.209 235.513 18.4784 21.0755 0.0929906 1

Total number of rows: 22575

Table truncated, full table size 8805 Kbytes.




Supplementary data files not provided
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