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Sample GSM39954 Query DataSets for GSM39954
Status Public on Feb 21, 2005
Title Lymph node, axillary 1187
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Lymph node, axillary 1187
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-10/34529.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 GPL1824
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
1 351 257 112 112 239 145 354 244 114 113 242 132 0 0 161 135 25 29 91 75 87 65 384 374 1.648 .607 .545 .544 .673 2.918 80 400 .682 .8 100 1650 8340 49 59 52 62 0 201 88 113 .474 191 103 2.11 .426 -1.077 -1.231 -1.077
2 304 168 113 116 191 52 309 171 117 119 196 55 0 0 74 61 31 35 98 59 92 30 243 251 3.673 .272 .281 .288 .327 2.898 52 278 .323 .6 90 1780 8330 48 57 65 74 0 131 91 41 .213 134 43 4.702 .219 -2.233 -2.189 -2.233
3 1169 1485 116 121 1053 1364 1157 1540 131 135 1041 1419 0 0 384 543 62 65 100 100 100 100 2417 2460 .772 1.295 1.363 1.269 1.362 1.499 80 393 1.343 .92 110 1930 8340 48 59 79 90 0 1160 95 1066 1.012 1203 1109 .988 1.065 .017 .091 .017
4 2900 6195 119 124 2781 6071 2827 5599 131 133 2708 5475 0 0 1786 4234 55 56 93 100 93 100 8852 8183 .458 2.183 2.022 1.87 2.13 2.142 80 365 2.469 .88 100 2070 8340 49 59 94 104 0 4840 97 4743 1.705 4374 4277 .586 1.58 .77 .659 .77
5 371 409 118 116 253 293 392 467 121 118 274 351 0 0 107 174 25 29 96 90 96 82 546 625 .863 1.158 1.281 .878 1.153 2.962 52 304 1.252 .83 90 2220 8330 48 57 109 118 0 320 91 229 .905 365 274 1.105 1.001 -.144 .001 -.144
6 307 225 120 116 187 109 323 226 127 124 203 110 0 0 92 68 85 70 81 68 58 37 296 313 1.716 .583 .542 .56 .574 2.038 80 353 .674 .84 100 2370 8340 49 59 124 134 0 176 91 85 .455 177 86 2.196 .423 -1.135 -1.24 -1.135
7 529 962 122 121 407 841 588 1077 132 131 466 956 0 0 196 364 91 72 90 96 83 92 1248 1422 .484 2.066 2.052 2.096 2.088 2.098 80 353 1.93 .91 100 2520 8340 49 59 139 149 0 752 95 657 1.614 841 747 .619 1.603 .691 .681 .691
8 2581 7511 119 121 2462 7390 2522 6405 123 126 2403 6284 0 0 1581 5068 34 33 100 100 100 100 9852 8687 .333 3.002 2.615 2.888 3.015 1.42 120 518 3.26 .94 120 2670 8320 46 58 153 165 0 5868 95 5773 2.345 5004 4909 .426 2.043 1.23 1.031 1.23
9 587 1309 121 125 466 1184 617 1330 123 130 496 1205 0 0 247 590 29 32 94 98 90 98 1650 1701 .394 2.541 2.429 2.638 2.618 1.842 52 283 2.557 .92 90 2800 8340 49 58 167 176 0 1023 98 925 1.985 1039 941 .504 1.898 .989 .924 .989
10 206 206 123 131 83 75 168 178 126 135 45 47 0 0 100 92 27 34 61 55 46 42 158 92 1.107 .904 1.044 1.072 1.112 3.049 52 276 .966 .68 80 2950 8330 49 57 183 191 -50 161 102 59 .706 139 37 1.417 .816 -.293 -.502
11 1403 1942 123 127 1280 1815 1455 2232 126 132 1332 2105 0 0 341 659 31 36 100 100 100 100 3095 3437 .705 1.418 1.58 1.344 1.427 1.412 80 457 1.528 .94 110 3110 8330 47 58 197 208 0 1517 99 1418 1.108 1744 1645 .903 1.235 .148 .304 .148
12 900 1292 127 125 773 1167 834 1183 139 154 707 1058 0 0 502 827 85 165 100 81 87 78 1940 1765 .662 1.51 1.496 1.281 1.544 2.169 32 176 1.647 .9 70 3230 8320 48 55 211 218 0 1009 98 912 1.179 924 827 .848 1.169 .238 .225 .238
13 579 762 124 125 455 637 607 795 134 140 483 670 0 0 316 381 67 123 84 90 80 75 1092 1153 .714 1.4 1.387 1.517 1.469 2.672 52 326 1.358 .89 90 3380 8340 49 58 225 234 0 595 98 498 1.094 621 523 .914 1.084 .129 .116 .129
14 308 238 126 134 182 104 322 248 127 137 196 114 0 0 138 116 30 34 84 65 75 59 286 310 1.75 .571 .582 .742 .785 2.187 32 156 .721 .75 60 3550 8340 51 57 244 250 0 186 105 81 .446 194 89 2.24 .454 -1.163 -1.138 -1.163
15 3549 6655 120 124 3429 6531 3847 6689 123 126 3727 6565 0 0 2358 4321 24 29 100 97 97 93 9960 10292 .525 1.905 1.761 1.933 1.938 2.461 80 405 1.946 .93 110 3680 8330 47 58 254 265 0 5199 97 5102 1.488 5226 5129 .672 1.376 .573 .461 .573
16 1452 1561 119 119 1333 1442 1618 1581 122 123 1499 1462 0 0 956 984 25 30 93 93 92 91 2775 2961 .924 1.082 .975 1.168 1.082 2.566 80 421 1.057 .93 110 3820 8330 47 58 268 279 0 1220 93 1127 .845 1235 1142 1.183 .762 -.243 -.392 -.243
17 295 241 128 133 167 108 320 264 136 137 192 131 0 0 84 70 43 38 90 81 81 75 275 323 1.546 .647 .682 .64 .697 1.778 32 207 .646 .71 70 3960 8330 49 56 284 291 0 188 104 84 .505 206 102 1.979 .533 -.985 -.908 -.985
18 301 207 124 136 177 71 318 221 130 140 194 85 0 0 128 95 40 39 82 63 75 53 248 279 2.493 .401 .438 .565 .574 2.192 52 271 .533 .74 80 4120 8330 49 57 300 308 0 162 106 55 .313 173 66 3.191 .342 -1.674 -1.547 -1.674
19 698 1374 119 129 579 1245 701 1421 121 131 582 1292 0 0 318 648 26 34 98 99 97 99 1824 1874 .465 2.15 2.22 2.284 2.144 2.015 120 490 2.257 .91 120 4280 8320 46 58 314 326 0 1073 101 973 1.68 1110 1009 .595 1.734 .748 .794 .748
20 278 210 122 140 156 70 275 224 125 143 153 84 0 0 129 84 29 35 76 69 73 55 226 237 2.229 .449 .549 .635 .541 2.594 52 218 .436 .62 80 4410 8330 49 57 329 337 -50 164 109 55 .351 175 66 2.853 .429 -1.221 -1.512

Total number of rows: 43008

Table truncated, full table size 9140 Kbytes.




Supplementary data files not provided
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