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Sample GSM39902 Query DataSets for GSM39902
Status Public on Feb 21, 2005
Title Uterus, endomyometrium 002B
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Uterus, endomyometrium 002B
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-01/24776.gif
 
Submission date Jan 26, 2005
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) pollack1@stanford.edu
Phone 650-736-1987
Organization name Stanford University
Department Pathology
Lab Pollack Lab
Street address 269 Campus Drive, CCSR3245A
City Stanford
State/province CA
ZIP/Postal code 94305-5176
Country USA
 
Platform ID GPL1823
Series (1)
GSE2193 Normal_human_tissues

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
VALUE same as UNF_VALUE but with flagged values removed
LOG_RAT2N_MEDIAN Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2
UNF_VALUE Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN VALUE LOG_RAT2N_MEDIAN UNF_VALUE
1 198 261 105 62 93 199 195 261 104 65 90 199 0 0 59 60 21 21 90 100 80 100 292 289 .467 2.14 2.211 2.57 2.259 2.302 52 278 2.082 .73 80 1430 7730 33 41 29 37 0 161 38 123 1.321 161 123 .757 1.365 .401 .449 .401
2 197 106 104 65 93 41 199 103 106 67 95 38 0 0 52 38 24 22 88 71 84 38 134 133 2.268 .441 .4 .413 .442 3.57 52 300 .332 .37 90 1580 7730 32 41 43 52 0 65 40 25 .272 64 23 3.675 .247 -1.878 -2.018 -1.878
3 285 457 102 66 183 391 276 458 105 67 174 392 0 0 68 121 24 21 100 100 100 100 574 566 .468 2.137 2.253 2.176 2.077 1.58 52 314 2.232 .84 90 1720 7730 32 41 57 66 0 282 41 241 1.319 283 242 .758 1.391 .399 .476 .399
4 882 1341 103 72 779 1269 851 1293 111 83 748 1221 0 0 394 634 54 87 100 100 100 100 2048 1969 .614 1.629 1.632 1.637 1.644 1.573 52 286 1.69 .93 80 1860 7730 33 41 72 80 0 828 44 783 1.006 798 754 .994 1.008 .008 .011 .008
5 248 169 115 88 133 81 233 169 123 98 118 81 0 0 82 38 55 94 78 37 53 0 214 199 1.642 .609 .686 .79 .488 3.452 32 224 .415 .58 70 2020 7720 32 39 88 95 0 104 54 50 .376 104 50 2.66 .424 -1.411 -1.239 -1.411
6 195 105 106 62 89 43 189 93 108 65 83 31 0 0 46 47 26 23 96 53 76 44 132 114 2.07 .483 .373 .388 .407 3.608 52 272 .452 .41 80 2170 7720 32 40 103 111 0 65 38 27 .298 57 19 3.353 .231 -1.745 -2.117 -1.745
7 948 272 102 64 846 208 268 134 109 69 166 70 0 0 2239 535 40 29 98 78 98 61 1054 236 4.067 .246 .422 .328 .369 2.63 52 287 .203 .84 90 2300 7720 31 40 115 124 -100 168 40 128 .152 83 43 6.589 .26 -1.942 -2.72
8 1136 2224 92 60 1044 2164 1074 2059 96 64 982 1999 0 0 439 988 23 23 100 100 100 100 3208 2981 .482 2.073 2.036 2.064 2.084 1.7 52 296 2.19 .92 90 2450 7720 31 40 130 139 0 1373 37 1336 1.28 1271 1234 .782 1.257 .356 .329 .356
9 245 269 93 56 152 213 232 265 95 60 139 209 0 0 72 84 21 21 98 100 96 98 365 348 .714 1.401 1.504 1.374 1.303 1.618 52 275 1.423 .81 80 2600 7730 33 41 146 154 0 166 35 131 .865 164 129 1.156 .928 -.209 -.108 -.209
10 201 106 94 59 107 47 206 102 96 62 112 43 0 0 46 35 20 19 93 78 93 56 154 155 2.277 .439 .384 .379 .432 2.211 32 215 .339 .49 70 2750 7720 32 39 161 168 0 65 36 29 .271 63 27 3.688 .237 -1.883 -2.077 -1.883
11 251 215 97 62 154 153 255 217 102 64 158 155 0 0 61 52 25 21 100 100 93 100 307 313 1.007 .994 .981 1.034 .97 1.698 32 210 .92 .77 70 2880 7730 33 40 174 181 0 133 38 94 .613 134 96 1.631 .606 -.705 -.724 -.705
12 265 255 98 58 167 197 264 231 100 61 166 173 0 0 74 117 23 21 98 100 98 100 364 339 .848 1.18 1.042 1.126 1.065 1.812 52 324 1.249 .81 90 3030 7730 32 41 188 197 0 157 36 122 .728 143 107 1.373 .643 -.458 -.636 -.458
13 219 186 98 59 121 127 219 188 99 62 121 129 0 0 58 63 22 21 98 94 90 92 248 250 .953 1.05 1.066 .946 .943 2.469 52 277 1.047 .74 80 3180 7720 32 40 204 212 0 115 36 78 .648 116 80 1.543 .658 -.626 -.604 -.626
14 196 120 99 63 97 57 202 110 101 65 103 47 0 0 46 44 23 22 93 78 87 53 154 150 1.702 .588 .456 .481 .392 3.646 32 199 .623 .44 70 3330 7730 33 40 219 226 0 74 39 35 .363 68 29 2.757 .282 -1.463 -1.828 -1.463
15 991 2093 102 61 889 2032 1021 2065 103 64 919 2004 0 0 349 782 24 21 100 100 100 100 2921 2923 .438 2.286 2.181 2.302 2.251 1.351 52 278 2.335 .96 90 3470 7730 32 41 232 241 0 1292 38 1254 1.411 1275 1237 .709 1.346 .497 .429 .497
16 346 418 104 66 242 352 354 382 106 68 250 316 0 0 103 132 25 27 100 100 98 100 594 566 .688 1.455 1.264 1.54 1.425 1.549 52 292 1.421 .89 90 3610 7730 32 41 246 255 0 258 41 217 .898 236 195 1.114 .78 -.155 -.358 -.155
17 170 111 104 63 66 48 163 103 108 66 59 40 0 0 49 37 25 29 87 62 65 28 114 99 1.375 .727 .678 .638 .531 3.601 32 220 .378 .34 70 3750 7720 32 39 261 268 0 69 39 30 .449 64 25 2.228 .418 -1.155 -1.257 -1.155
18 172 101 100 65 72 36 173 88 102 68 73 23 0 0 32 40 21 24 93 46 75 31 108 96 2 .5 .315 .551 .496 3.511 32 222 .5 .16 70 3910 7720 32 39 277 284 0 62 40 22 .309 54 14 3.24 .194 -1.696 -2.362 -1.696
19 207 167 101 67 106 100 208 166 104 69 107 99 0 0 68 55 23 21 90 90 84 87 206 206 1.06 .943 .925 .79 .893 2.565 32 222 .719 .61 70 4050 7720 32 39 291 298 0 103 41 62 .582 102 61 1.717 .571 -.78 -.808 -.78
20 172 116 96 65 76 51 171 94 100 67 75 29 0 0 43 53 24 21 87 68 75 37 127 104 1.49 .671 .387 .625 .502 5.075 32 226 .548 .26 70 4200 7720 32 39 306 313 0 72 40 31 .414 58 18 2.414 .239 -1.271 -2.067 -1.271

Total number of rows: 43008

Table truncated, full table size 9069 Kbytes.




Supplementary data files not provided
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