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Sample GSM39933 Query DataSets for GSM39933
Status Public on Feb 21, 2005
Title Lymph node 1337
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Lymph node 1337
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-10/34531.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
1 490 398 121 143 369 255 553 430 136 152 432 287 0 0 233 216 70 68 82 76 78 65 624 719 1.447 .691 .664 .656 .696 1.623 52 350 .742 .74 90 1780 9010 64 73 41 50 0 415 149 266 .72 448 299 1.389 .692 -.474 -.531 -.474
2 394 293 126 127 268 166 441 286 326 384 315 159 0 0 160 131 993 1254 0 0 0 0 434 474 1.614 .619 .505 .603 .637 2.241 80 362 .641 .67 100 1940 9020 65 75 57 67 0 305 132 173 .645 298 166 1.55 .526 -.632 -.927 -.632
3 1581 1174 113 138 1468 1036 1850 1073 129 154 1737 935 0 0 1039 786 90 109 85 85 80 80 2504 2672 1.417 .706 .538 .773 .723 3.558 120 406 .686 .83 120 2080 9010 63 75 70 82 0 1223 144 1079 .735 1118 974 1.36 .561 -.444 -.835 -.444
4 2917 3419 112 133 2805 3286 1846 2227 121 140 1734 2094 0 0 2697 3281 40 64 92 88 87 82 6091 3828 .854 1.171 1.208 .981 1.133 4 80 306 1.222 .91 100 2220 9010 64 74 85 95 0 3561 139 3423 1.22 2320 2181 .819 1.258 .287 .331 .287
5 444 721 117 140 327 581 489 635 130 154 372 495 0 0 220 448 65 80 83 85 78 75 908 867 .563 1.777 1.331 1.472 1.757 2.516 80 367 2.051 .83 110 2370 9020 64 75 99 110 0 751 146 605 1.851 661 516 .54 1.386 .888 .471 .888
6 460 521 125 151 335 370 546 554 143 162 421 403 0 0 218 322 69 76 76 71 75 69 705 824 .905 1.104 .957 1.057 1.28 2.809 52 292 1.581 .72 90 2510 9010 64 73 114 123 0 543 157 385 1.15 577 420 .869 .997 .202 -.004 .202
7 658 3057 121 156 537 2901 745 3601 133 172 624 3445 0 0 327 1720 57 86 86 95 82 93 3438 4069 .185 5.402 5.521 4.996 5.503 3.009 80 352 6.244 .85 100 2670 9020 65 75 130 140 0 3184 163 3022 5.627 3751 3589 .178 5.751 2.492 2.524 2.492
8 6609 8315 118 169 6491 8146 7323 9160 133 186 7205 8991 0 0 3761 5546 62 85 100 96 100 95 14637 16196 .797 1.255 1.248 1.142 1.318 2.419 80 415 1.398 .84 110 2810 9010 63 74 143 154 0 8661 176 8485 1.307 9542 9366 .765 1.3 .387 .378 .387
9 798 860 138 178 660 682 876 992 167 187 738 814 0 0 351 415 105 88 90 87 81 78 1342 1552 .968 1.033 1.103 .92 1.063 2.751 32 186 1.06 .81 70 2950 9030 67 74 159 166 0 896 185 710 1.076 1033 848 .929 1.149 .106 .2 .106
10 255 212 136 164 119 48 202 185 154 184 66 21 0 0 145 110 77 186 44 5 38 1 167 87 2.479 .403 .318 .771 .692 2.954 52 287 .575 .38 80 3090 9010 65 73 173 181 -50 221 171 50 .42 193 22 2.38 .331 -1.593 -1.251
11 1443 1178 126 169 1317 1009 1659 1315 144 198 1533 1146 0 0 639 626 85 173 95 83 91 77 2326 2679 1.305 .766 .748 .715 .79 1.993 80 447 .832 .85 110 3260 9010 63 74 188 199 0 1227 176 1051 .798 1370 1194 1.253 .779 -.325 -.361 -.325
12 767 768 134 170 633 598 505 508 140 178 371 338 0 0 598 579 41 63 88 80 86 71 1231 709 1.059 .945 .911 .82 .937 2.966 52 224 .961 .86 80 3380 9010 65 73 202 210 0 800 177 623 .984 529 352 1.016 .949 -.023 -.076 -.023
13 696 584 132 175 564 409 748 596 139 180 616 421 0 0 324 340 42 64 86 78 86 73 973 1037 1.379 .725 .683 .771 .831 2.544 52 333 .833 .86 90 3530 9020 65 74 216 225 0 608 182 426 .755 621 439 1.324 .712 -.405 -.49 -.405
14 460 370 153 182 307 188 527 360 168 187 374 178 0 0 147 155 60 70 91 83 75 75 495 552 1.633 .612 .476 .73 .579 1.68 12 92 .761 .75 50 3700 9010 66 71 235 240 0 385 190 196 .638 375 185 1.568 .496 -.649 -1.012 -.649
15 4661 4803 121 157 4540 4646 5147 5296 130 165 5026 5139 0 0 3202 3213 44 56 96 92 91 90 9186 10165 .977 1.023 1.022 1.029 .935 3.366 80 355 1.013 .85 100 3830 9010 64 74 246 256 0 5003 164 4840 1.066 5517 5353 .938 1.065 .092 .091 .092
16 1725 1350 116 155 1609 1195 1988 1659 120 165 1872 1504 0 0 1085 780 33 58 91 88 87 86 2804 3376 1.346 .743 .803 .655 .692 2.762 80 372 .677 .83 100 3970 9010 64 74 260 270 0 1406 161 1245 .774 1728 1567 1.293 .837 -.37 -.257 -.37
17 362 327 121 171 241 156 393 321 138 184 272 150 0 0 128 125 74 62 87 78 78 59 397 422 1.545 .647 .551 .564 .654 2.362 32 156 .633 .63 60 4100 9010 66 72 275 281 0 341 178 163 .674 334 156 1.483 .574 -.569 -.8 -.569
18 289 208 112 155 177 53 286 193 125 162 174 38 0 0 134 81 50 61 75 40 75 18 230 212 3.34 .299 .218 .326 .341 1.98 32 225 .428 .47 70 4260 9010 65 72 290 297 0 217 161 55 .312 201 40 3.206 .227 -1.681 -2.136 -1.681
19 1139 1184 113 153 1026 1031 1224 1272 117 160 1111 1119 0 0 380 456 32 54 100 100 100 98 2057 2230 .995 1.005 1.007 .963 1.033 1.663 80 393 1.049 .89 100 4420 9010 64 74 305 315 0 1233 159 1074 1.047 1325 1166 .955 1.049 .066 .069 .066
20 435 367 115 158 320 209 451 360 115 163 336 202 0 0 98 129 27 51 98 90 96 82 529 538 1.531 .653 .601 .613 .612 2.42 52 254 .731 .72 80 4560 9010 65 73 320 328 0 382 165 218 .68 375 210 1.47 .626 -.556 -.675 -.556

Total number of rows: 43008

Table truncated, full table size 9346 Kbytes.




Supplementary data files not provided
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