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Sample GSM39915 Query DataSets for GSM39915
Status Public on Feb 21, 2005
Title Kidney 0265
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Kidney 0265
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-03/26613.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
1 202 263 109 147 93 116 191 259 110 151 82 112 0 0 38 53 22 30 98 96 92 86 209 194 .802 1.247 1.366 1.197 1.238 1.777 52 293 1.471 .75 80 1280 7840 36 44 32 40 0 277 155 122 1.313 273 118 .762 1.438 .393 .524 .393
2 196 176 115 142 81 34 198 177 121 145 83 35 0 0 27 37 32 28 100 50 75 33 115 118 2.382 .42 .422 .506 .62 2.982 12 98 .562 .19 50 1400 7840 37 42 45 50 0 185 149 36 .442 186 37 2.263 .444 -1.178 -1.172 -1.178
3 490 709 104 148 386 561 538 712 109 150 434 564 0 0 206 318 27 32 97 93 93 93 947 998 .688 1.453 1.3 1.401 1.497 1.719 80 388 1.535 .93 100 1570 7840 35 45 60 70 0 746 156 591 1.53 749 594 .654 1.368 .613 .452 .613
4 1405 2003 104 150 1301 1853 1335 1909 106 153 1231 1759 0 0 939 1310 22 32 96 100 95 100 3154 2990 .702 1.424 1.429 1.625 1.436 1.985 80 340 1.445 .94 100 1710 7830 34 44 74 84 0 2108 158 1951 1.499 2009 1852 .667 1.504 .584 .589 .584
5 258 400 102 153 156 247 271 409 104 157 169 256 0 0 55 103 21 31 100 100 100 98 403 425 .632 1.583 1.515 1.515 1.531 1.585 52 230 1.907 .84 80 1860 7840 36 44 90 98 0 421 161 260 1.667 431 269 .6 1.595 .737 .673 .737
6 145 165 106 152 39 13 148 155 107 155 42 3 0 0 43 33 21 31 63 31 50 7 52 45 3 .333 .071 .568 .727 3.405 80 353 .643 .28 100 1990 7840 35 45 102 112 -50 174 160 14 .351 163 3 2.85 .075 -3.733 -1.511
7 352 194 109 158 243 36 368 191 116 159 259 33 0 0 104 40 37 40 96 43 93 12 279 292 6.75 .148 .127 .172 .173 2.377 32 207 .113 .37 70 2140 7840 36 43 118 125 0 204 166 38 .156 201 35 6.413 .134 -2.681 -2.898 -2.681
8 1830 1367 102 160 1728 1207 1648 1174 107 161 1546 1014 0 0 1300 941 33 36 96 98 95 98 2935 2560 1.432 .698 .656 .762 .672 1.76 80 371 .704 .98 100 2300 7830 34 44 133 143 0 1439 168 1271 .735 1236 1067 1.36 .69 -.444 -.534 -.444
9 489 792 98 168 391 624 533 806 100 173 435 638 0 0 153 270 21 39 98 100 96 100 1015 1073 .627 1.596 1.467 1.634 1.67 1.673 52 211 1.685 .94 80 2440 7840 36 44 148 156 0 834 177 657 1.68 848 672 .595 1.544 .748 .627 .748
10 162 239 105 206 57 33 141 203 107 207 36 -3 0 0 70 98 23 39 52 36 45 28 90 33 1.727 .579 null 1.218 1.175 3.015 80 345 1.566 .48 100 2580 7830 34 44 161 171 -50 252 217 35 .609 214 null 1.641 null null -.714
11 494 509 94 170 400 339 477 501 96 177 383 331 0 0 180 190 23 44 94 94 94 92 739 714 1.18 .848 .864 .826 .835 1.497 52 233 .905 .92 80 2730 7840 36 44 177 185 0 536 179 357 .892 527 348 1.121 .91 -.165 -.137 -.165
12 537 376 89 148 448 228 514 363 90 149 425 215 0 0 173 121 19 27 100 94 98 94 676 640 1.965 .509 .506 .483 .517 1.399 52 242 .538 .93 80 2870 7840 36 44 191 199 0 396 156 240 .536 382 226 1.867 .533 -.9 -.909 -.9
13 324 295 89 153 235 142 331 280 91 154 242 127 0 0 97 99 19 28 96 92 96 80 377 369 1.655 .604 .525 .529 .567 1.861 52 252 .716 .83 80 3020 7840 36 44 206 214 0 311 161 149 .636 295 134 1.572 .552 -.653 -.856 -.653
14 165 232 88 155 77 77 160 222 89 155 72 67 0 0 34 55 19 29 94 84 88 55 154 139 1 1 .931 .874 .955 1.965 52 219 1.401 .65 80 3170 7840 36 44 221 229 0 244 163 81 1.053 234 71 .95 .98 .074 -.03 .074
15 1487 1582 93 154 1394 1428 1625 1589 93 155 1532 1435 0 0 1001 905 21 29 92 96 92 95 2822 2967 .976 1.024 .937 1.223 1.004 2.103 80 349 .972 .96 100 3300 7830 34 44 233 243 0 1665 162 1503 1.078 1673 1511 .927 .986 .109 -.02 .109
16 556 634 91 155 465 479 590 629 94 157 499 474 0 0 169 172 23 29 100 100 100 100 944 973 .971 1.03 .95 1.066 .948 1.726 52 288 .974 .89 90 3460 7830 34 43 249 258 0 667 163 504 1.084 662 499 .922 1 .117 0 .117
17 130 140 88 155 42 -15 132 140 92 154 44 -15 0 0 33 28 21 29 68 5 52 0 27 29 null null null .386 .209 5.292 80 348 1.253 .09 100 3600 7830 34 44 263 273 -50 147 163 -16 null 147 null null null null null
18 119 160 88 149 31 11 113 156 90 150 25 7 0 0 35 35 18 30 56 28 38 8 42 32 2.818 .355 .28 .964 .833 3.346 80 368 2.704 .12 100 3750 7830 34 44 278 288 -50 168 157 12 .374 164 7 2.677 .295 -1.763 -1.421
19 306 399 85 153 221 246 307 385 90 156 222 232 0 0 140 148 24 30 100 93 81 93 467 454 .898 1.113 1.045 1.238 1.172 1.763 32 192 1.065 .84 70 3890 7830 35 42 293 300 0 420 161 259 1.172 405 244 .853 1.1 .229 .138 .229
20 121 176 86 159 35 17 122 174 89 161 36 15 0 0 35 49 22 31 60 33 42 13 52 51 2.059 .486 .417 .83 .691 3.367 80 383 3.355 .16 100 4040 7830 34 44 307 317 -50 185 167 18 .511 183 16 1.956 .439 -1.189 -.968

Total number of rows: 43008

Table truncated, full table size 9119 Kbytes.




Supplementary data files not provided
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