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Sample GSM39889 Query DataSets for GSM39889
Status Public on Feb 21, 2005
Title Uterus, endomyometrium 0002
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Uterus, endomyometrium 0002
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-02/25137.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
1 130 207 83 96 47 111 127 200 85 98 44 104 0 0 33 40 16 18 84 100 65 98 158 148 .423 2.362 2.364 2.465 2.508 2.008 52 245 2.79 .6 80 1460 8170 53 61 86 94 0 205 95 110 2.338 198 103 .428 2.34 1.225 1.227 1.225
2 106 78 85 96 21 -18 107 76 86 98 22 -20 0 0 26 23 16 17 55 8 33 2 3 2 null null null 2.05 2.049 3.19 80 345 1.014 .43 100 1600 8160 51 61 99 109 -50 77 95 -18 null 75 null null null null null
3 250 306 85 98 165 208 262 313 86 99 177 215 0 0 71 93 16 19 98 96 96 96 373 392 .793 1.261 1.215 1.253 1.245 1.489 52 242 1.312 .88 80 1750 8170 53 61 115 123 0 303 97 206 1.248 310 213 .801 1.203 .32 .266 .32
4 866 888 87 98 779 790 876 927 88 99 789 829 0 0 508 503 18 17 95 98 90 97 1569 1618 .986 1.014 1.051 1.082 .976 2.258 80 382 1.003 .94 100 1910 8170 52 62 130 140 0 879 97 782 1.004 918 821 .996 1.04 .006 .057 .006
5 151 123 86 99 65 24 150 120 87 99 64 21 0 0 37 22 18 19 87 50 71 34 89 85 2.708 .369 .328 .365 .361 2.942 32 187 .372 .39 70 2050 8170 53 60 145 152 0 122 98 24 .366 119 21 2.735 .325 -1.452 -1.622 -1.452
6 113 93 86 96 27 -3 108 88 87 97 22 -8 0 0 31 31 16 19 61 18 42 7 24 14 null null null 1.061 .9 3.209 80 378 2.361 .09 100 2180 8160 51 61 157 167 -50 92 95 -3 null 87 null null null null null
7 201 88 87 97 114 -9 205 83 92 99 118 -14 0 0 59 23 26 19 92 17 84 3 105 104 null null null .283 .33 3.612 52 319 8.199 .3 90 2340 8170 52 61 173 182 0 87 96 -9 null 82 null null null null null null
8 865 1221 85 98 780 1123 899 1218 87 100 814 1120 0 0 490 707 17 18 96 98 95 97 1903 1934 .695 1.44 1.376 1.562 1.438 1.838 80 313 1.454 .96 100 2490 8170 52 62 188 198 0 1209 97 1112 1.425 1206 1109 .702 1.362 .511 .446 .511
9 227 199 86 99 141 100 234 201 87 101 148 102 0 0 67 39 18 20 96 98 92 90 241 250 1.41 .709 .689 .756 .702 1.824 52 240 .642 .84 80 2630 8170 53 61 203 211 0 197 98 99 .702 199 101 1.424 .682 -.51 -.551 -.51
10 145 93 94 105 51 -12 144 94 97 106 50 -11 0 0 22 15 22 17 100 0 58 0 39 39 null null null .2 .241 2.433 12 100 12.258 .08 50 2790 8170 54 59 220 225 0 92 104 -12 null 93 null null null null null null
11 271 259 87 104 184 155 283 262 89 105 196 158 0 0 79 56 16 19 93 100 93 96 339 354 1.187 .842 .806 .895 .862 1.588 32 142 .847 .87 60 2920 8180 55 61 233 239 0 256 103 153 .834 259 156 1.199 .798 -.262 -.325 -.262
12 333 336 89 108 244 228 350 337 90 108 261 229 0 0 104 74 17 18 100 100 100 100 472 490 1.07 .934 .877 .997 .94 1.622 52 310 .884 .89 90 3060 8170 52 61 245 254 0 333 107 226 .925 334 227 1.081 .869 -.112 -.203 -.112
13 216 175 89 104 127 71 219 180 90 105 130 76 0 0 53 35 17 17 96 93 90 87 198 206 1.789 .559 .585 .558 .567 1.693 32 220 .519 .76 70 3220 8170 53 60 262 269 0 173 103 70 .554 178 75 1.807 .579 -.853 -.789 -.853
14 147 114 89 108 58 6 146 112 90 109 57 4 0 0 33 22 17 20 87 18 78 6 64 61 9.667 .103 .07 .209 .169 4.938 32 146 .046 .05 60 3360 8160 53 59 277 283 0 113 107 6 .102 111 4 9.763 .069 -3.287 -3.847 -3.287
15 1284 1484 88 113 1196 1371 1425 1700 92 115 1337 1587 0 0 734 880 18 21 97 92 96 90 2567 2924 .872 1.146 1.187 .98 1.109 2.121 80 340 1.181 .94 100 3500 8160 51 61 289 299 0 1469 112 1357 1.135 1683 1571 .881 1.175 .183 .233 .183
16 456 457 88 113 368 344 492 478 90 114 404 365 0 0 135 115 18 18 98 100 94 100 712 769 1.07 .935 .903 .959 .923 1.411 52 248 .875 .91 90 3650 8170 52 61 304 313 0 452 112 341 .926 473 361 1.08 .895 -.112 -.161 -.112
17 104 101 89 113 15 -12 99 101 90 115 10 -12 0 0 24 23 18 20 40 11 22 1 3 -2 null null null 1.182 1.388 4.722 80 316 .557 .21 100 3790 8150 50 60 318 328 -50 100 112 -12 null 100 null null null null null
18 103 100 89 114 14 -14 102 101 91 116 13 -13 0 0 25 27 22 22 36 12 7 2 0 0 null null null 1.188 1.15 3.185 80 374 .369 .14 100 3930 8150 50 60 332 342 -50 99 113 -14 null 100 null null null null null
19 280 307 90 111 190 196 265 306 99 112 175 195 0 0 80 107 30 22 100 100 100 91 386 370 .969 1.032 1.114 .924 .92 1.585 12 90 1.178 .88 50 4100 8170 54 59 351 356 0 304 110 194 1.021 303 193 .979 1.103 .03 .142 .03
20 109 105 86 113 23 -8 100 106 88 115 14 -7 0 0 30 20 17 20 47 8 32 0 15 7 null null null 1.025 1.22 3.661 80 399 2.244 .13 100 4220 8150 50 60 361 371 -50 104 112 -8 null 105 null null null null null

Total number of rows: 43008

Table truncated, full table size 8947 Kbytes.




Supplementary data files not provided
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