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Sample GSM39916 Query DataSets for GSM39916
Status Public on Feb 21, 2005
Title Prostate 1277
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Prostate 1277
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-01/24475.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
1 275 176 125 98 150 78 274 172 130 100 149 74 0 0 68 41 34 21 96 87 90 78 228 223 1.923 .52 .497 .449 .511 1.99 32 220 .472 .73 70 1530 7920 44 51 41 48 0 147 82 65 .433 143 62 2.308 .414 -1.206 -1.273 -1.206
2 227 140 126 99 101 41 233 140 129 102 107 41 0 0 43 25 31 23 90 71 81 37 142 148 2.463 .406 .383 .382 .331 2.699 32 215 .488 .52 70 1670 7920 44 51 55 62 0 117 83 34 .338 117 34 2.956 .319 -1.564 -1.647 -1.564
3 684 713 131 99 553 614 740 753 135 100 609 654 0 0 231 212 29 19 100 100 96 100 1167 1263 .901 1.11 1.074 1.217 1.143 1.523 52 329 1.067 .93 90 1820 7910 42 51 69 78 0 594 83 512 .925 628 545 1.081 .895 -.112 -.16 -.112
4 1402 3901 135 104 1267 3797 1316 3861 138 105 1181 3757 0 0 882 2324 31 21 98 100 95 100 5064 4938 .334 2.997 3.181 3.392 2.849 1.973 80 419 2.961 .96 100 1970 7910 42 52 84 94 0 3251 87 3164 2.497 3218 3131 .4 2.651 1.32 1.407 1.32
5 293 371 137 108 156 263 316 400 139 112 179 292 0 0 109 110 29 34 84 93 84 90 419 471 .593 1.686 1.631 1.733 1.465 2.222 32 164 1.468 .84 60 2110 7920 45 51 100 106 0 309 90 219 1.405 333 243 .712 1.359 .49 .443 .49
6 227 160 137 101 90 59 247 163 141 102 110 62 0 0 73 36 31 20 78 93 65 68 149 172 1.525 .656 .564 .679 .638 2.786 32 176 .411 .54 60 2250 7910 44 50 114 120 0 133 84 49 .546 136 52 1.831 .47 -.872 -1.09 -.872
7 337 233 143 107 194 126 360 245 148 111 217 138 0 0 101 54 37 28 86 94 82 84 320 355 1.54 .649 .636 .682 .641 2.403 52 270 .568 .84 80 2400 7910 43 51 128 136 0 194 89 105 .541 204 115 1.848 .53 -.886 -.916 -.886
8 1807 3346 125 92 1682 3254 1881 3411 129 95 1756 3319 0 0 790 1405 28 23 100 100 100 100 4936 5075 .517 1.935 1.89 2.032 1.934 1.272 52 318 1.907 .98 90 2550 7900 41 50 142 151 0 2788 77 2712 1.612 2843 2766 .62 1.575 .689 .655 .689
9 527 720 121 88 406 632 563 738 125 89 442 650 0 0 170 261 27 18 100 100 100 100 1038 1092 .642 1.557 1.471 1.541 1.528 1.484 52 254 1.594 .95 80 2690 7910 43 51 157 165 0 600 73 527 1.297 615 542 .771 1.225 .375 .293 .375
10 223 235 122 92 101 143 226 236 125 93 104 144 0 0 62 62 26 20 90 100 76 96 244 248 .706 1.416 1.385 1.492 1.372 1.86 52 242 1.239 .8 80 2840 7910 43 51 172 180 0 196 77 119 1.18 197 120 .848 1.154 .239 .206 .239
11 446 487 118 91 328 396 480 543 120 92 362 452 0 0 227 224 24 20 94 100 86 100 724 814 .828 1.207 1.249 1.247 1.128 1.605 52 314 1.134 .92 90 2970 7910 42 51 184 193 0 406 76 330 1.006 453 377 .994 1.041 .009 .057 .009
12 532 539 117 90 415 449 528 558 119 92 411 468 0 0 153 168 23 22 98 100 98 100 864 879 .924 1.082 1.139 1.121 1.087 1.677 52 322 1.101 .94 90 3130 7910 42 51 200 209 0 449 75 374 .902 465 390 1.109 .949 -.149 -.076 -.149
13 366 443 120 93 246 350 405 468 123 95 285 375 0 0 129 166 25 20 92 100 90 100 596 660 .703 1.423 1.316 1.511 1.343 1.883 52 242 1.399 .91 80 3270 7910 43 51 215 223 0 369 78 292 1.186 390 313 .843 1.096 .246 .133 .246
14 231 155 121 93 110 62 238 150 123 94 117 57 0 0 59 31 25 19 90 92 86 71 172 174 1.774 .564 .487 .521 .503 1.935 52 288 .463 .64 90 3420 7910 42 51 229 238 0 129 78 52 .47 125 48 2.129 .406 -1.09 -1.301 -1.09
15 1580 2335 122 101 1458 2234 1737 2590 123 102 1615 2489 0 0 878 1182 26 22 97 100 96 100 3692 4104 .653 1.532 1.541 1.771 1.52 1.912 80 383 1.49 .97 100 3560 7910 42 52 243 253 0 1946 84 1862 1.277 2158 2074 .783 1.284 .353 .361 .353
16 803 1641 124 100 679 1541 864 1807 127 101 740 1707 0 0 236 499 29 21 96 100 94 100 2220 2447 .441 2.27 2.307 2.33 2.308 1.466 52 347 2.383 .95 90 3720 7910 42 51 259 268 0 1368 83 1284 1.891 1506 1423 .529 1.922 .919 .943 .919
17 217 148 125 97 92 51 222 152 126 99 97 55 0 0 51 36 30 22 90 78 87 62 143 152 1.804 .554 .567 .555 .63 1.865 32 183 .585 .57 70 3870 7920 44 51 275 282 0 123 81 43 .462 127 46 2.165 .473 -1.114 -1.082 -1.114
18 222 133 128 105 94 28 234 132 140 120 106 27 0 0 59 33 121 172 38 0 0 0 122 133 3.357 .298 .255 .357 .365 2.162 52 249 .261 .41 80 4000 7910 43 51 288 296 0 111 88 23 .248 110 23 4.029 .212 -2.01 -2.236 -2.01
19 401 559 127 101 274 458 441 630 130 101 314 529 0 0 165 237 26 23 90 93 90 93 732 843 .598 1.672 1.685 1.513 1.742 1.517 32 214 1.609 .9 70 4140 7920 44 51 302 309 0 466 84 382 1.393 525 441 .718 1.404 .478 .489 .478
20 224 134 128 106 96 28 243 137 128 107 115 31 0 0 62 29 23 20 84 59 81 34 124 146 3.429 .292 .27 .346 .367 1.802 32 151 .319 .49 60 4300 7910 44 50 319 325 0 112 88 23 .243 114 26 4.114 .225 -2.041 -2.154 -2.041

Total number of rows: 43008

Table truncated, full table size 9026 Kbytes.




Supplementary data files not provided
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