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Sample GSM90120 Query DataSets for GSM90120
Status Public on Dec 30, 2005
Title PN187_7
Sample type RNA
 
Channel 1
Source name CRG
Organism Homo sapiens
Characteristics CRG
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name PN187_7
Organism Homo sapiens
Characteristics PN187_7
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Prostate, Non-tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/29164.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Dec 29, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL3044
Series (1)
GSE3933 Prostate Cancer

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
LOG_RAT2N_MEAN 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
VALUE 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

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 LOG_RAT2N_MEAN VALUE
1 130 159 74 49 56 110 126 155 77 53 52 106 0 0 51 66 20 22 73 92 59 76 166 158 .509 1.964 2.038 1.884 1.921 3.14 52 338 1.706 .61 90 1760 8750 190 199 39 48 0 135 42 93 1.665 131 90 .601 1.728 .735 .789
2 192 184 73 52 119 132 120 160 78 57 47 108 0 0 271 138 28 27 69 92 36 78 251 155 .902 1.109 2.298 2.114 3.077 3.145 52 256 .401 .45 80 1900 8770 193 201 54 62 -100 156 44 112 .94 136 92 1.064 1.947 -.089 .962
3 271 222 69 51 202 171 230 195 74 55 161 144 0 0 171 130 25 24 95 95 90 86 373 305 1.181 .847 .894 .834 .877 2.465 80 409 .799 .81 110 2060 8750 189 200 68 79 0 188 43 145 .717 165 122 1.394 .758 -.479 -.4
4 396 491 70 49 326 442 377 445 74 54 307 396 0 0 248 325 23 25 87 97 85 91 768 703 .738 1.356 1.29 1.303 1.254 2.842 80 373 1.412 .82 100 2200 8760 191 201 83 93 0 416 42 375 1.149 377 336 .87 1.093 .2 .128
5 132 170 69 47 63 123 126 159 71 50 57 112 0 0 55 84 21 20 73 90 55 84 186 169 .512 1.952 1.965 2.158 2.287 3.832 52 254 2.179 .56 80 2350 8760 192 200 99 107 0 144 40 104 1.655 135 95 .604 1.665 .726 .736
6 107 153 68 49 39 104 110 152 71 52 42 103 0 0 27 69 19 21 75 86 55 78 143 145 .375 2.667 2.452 2.082 2.791 2.797 52 282 3.711 .5 80 2490 8760 192 200 113 121 0 130 42 88 2.26 129 87 .443 2.078 1.176 1.055
7 205 155 71 50 134 105 208 147 73 53 137 97 0 0 78 46 22 21 86 100 82 94 239 234 1.276 .784 .708 .845 .773 2.721 52 323 .603 .62 90 2640 8750 190 199 127 136 0 131 42 89 .664 125 82 1.506 .6 -.591 -.737
8 583 866 71 48 512 818 589 750 74 52 518 702 0 0 353 526 22 30 93 100 87 98 1330 1220 .626 1.598 1.355 1.798 1.513 2.879 80 400 1.703 .8 100 2780 8760 191 201 141 151 0 734 41 693 1.354 636 595 .739 1.148 .437 .2
9 228 206 75 49 153 157 226 207 79 57 151 158 0 0 84 82 25 35 92 96 82 82 310 309 .975 1.026 1.046 1.002 1.041 2.918 52 358 1.074 .71 90 2940 8750 190 199 157 166 0 175 42 133 .87 175 134 1.15 .887 -.202 -.173
10 137 149 75 58 62 91 135 144 79 67 60 86 0 0 34 59 31 40 83 75 50 58 153 146 .681 1.468 1.433 1.409 1.462 3.695 12 86 2.191 .42 50 3090 8740 191 196 174 179 0 126 49 77 1.244 122 73 .804 1.215 .315 .281
11 291 257 73 50 218 207 226 242 76 53 153 192 0 0 147 121 20 23 97 98 95 93 425 345 1.053 .95 1.255 1.009 .956 1.895 80 467 .866 .84 110 3210 8750 189 200 183 194 0 218 42 175 .805 205 163 1.243 1.063 -.313 .089
12 175 187 76 52 99 135 177 185 77 55 101 133 0 0 59 56 19 22 92 100 82 96 234 234 .733 1.364 1.317 1.448 1.386 2.333 52 285 1.289 .67 90 3370 8750 190 199 200 209 0 158 44 114 1.156 157 113 .865 1.116 .209 .158
13 198 201 76 53 122 148 193 201 78 56 117 148 0 0 85 88 20 23 88 96 76 84 270 265 .824 1.213 1.265 1.249 1.056 2.527 52 259 1.123 .7 90 3500 8760 191 200 213 222 0 170 45 125 1.028 170 125 .973 1.072 .04 .1
14 120 214 76 52 44 162 118 213 78 57 42 161 0 0 37 82 21 23 65 94 50 94 206 203 .272 3.682 3.833 3.795 3 2.654 52 323 3.423 .58 90 3650 8760 191 200 228 237 0 181 44 137 3.12 181 136 .32 3.249 1.642 1.7
15 588 602 72 53 516 549 527 602 75 58 455 549 0 0 387 367 20 24 96 100 92 97 1065 1004 .94 1.064 1.207 1.125 1.116 2.201 80 412 1.047 .86 110 3800 8750 189 200 242 253 0 510 45 465 .902 510 465 1.109 1.023 -.149 .032
16 209 325 69 51 140 274 186 310 72 54 117 259 0 0 86 131 19 20 97 98 91 98 414 376 .511 1.957 2.214 2.04 1.959 2.173 80 421 2.429 .71 110 3930 8750 189 200 255 266 0 275 43 232 1.659 263 219 .603 1.876 .73 .908
17 103 129 71 52 32 77 104 126 73 57 33 74 0 0 28 40 19 22 71 90 42 76 109 107 .416 2.406 2.242 2.227 1.728 3.36 52 282 3.232 .36 80 4090 8750 191 199 273 281 0 109 44 65 2.039 107 63 .49 1.9 1.028 .926
18 110 135 75 60 35 75 111 135 78 62 36 75 0 0 27 49 22 27 68 84 28 68 110 111 .467 2.143 2.083 2.243 1.944 2.961 32 204 3.379 .35 70 4250 8750 191 198 289 296 0 114 51 64 1.816 114 64 .551 1.766 .861 .82
19 272 336 73 56 199 280 264 296 77 59 191 240 0 0 119 173 23 24 97 98 91 97 479 431 .711 1.407 1.257 1.419 1.432 2.279 80 399 1.587 .76 100 4390 8740 189 199 302 312 0 285 47 237 1.192 251 203 .839 1.065 .254 .091
20 115 137 76 52 39 85 110 135 78 54 34 83 0 0 32 40 21 18 65 98 42 86 124 117 .459 2.179 2.441 2.392 2.368 2.879 52 227 2.426 .42 80 4530 8760 192 200 317 325 0 116 44 72 1.847 114 70 .541 2.069 .885 1.049

Total number of rows: 43008

Table truncated, full table size 8888 Kbytes.




Supplementary data files not provided
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