NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM90121 Query DataSets for GSM90121
Status Public on Dec 30, 2005
Title PN190_4
Sample type RNA
 
Channel 1
Source name CRG
Organism Homo sapiens
Characteristics CRG
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name PN190_4
Organism Homo sapiens
Characteristics PN190_4
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Prostate, Non-tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/29167.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
1 387 204 202 84 185 120 417 198 204 88 215 114 0 0 128 82 39 30 80 86 75 75 305 329 1.542 .649 .53 .671 .541 3.066 52 276 .481 .61 80 1760 8540 170 178 40 48 0 171 71 101 .545 166 96 1.835 .446 -.875 -1.166
2 281 177 195 87 86 90 267 160 198 92 72 73 0 0 57 70 42 34 80 80 46 51 176 145 .956 1.047 1.014 .953 1.014 3.026 52 223 .752 .37 80 1900 8530 169 177 54 62 0 149 73 76 .879 134 61 1.137 .852 -.185 -.231
3 1745 1134 192 86 1553 1048 1939 1166 215 99 1747 1080 0 0 752 486 157 81 95 98 88 95 2601 2827 1.482 .675 .618 .709 .643 2.283 80 441 .618 .87 110 2020 8530 167 178 64 75 0 953 72 881 .567 980 908 1.763 .519 -.818 -.945
4 3843 5695 196 84 3647 5611 3148 5122 222 97 2952 5038 0 0 2911 4614 170 87 96 97 86 92 9258 7990 .65 1.539 1.707 1.471 1.57 3.925 80 361 1.711 .82 100 2190 8540 169 179 82 92 0 4786 71 4715 1.293 4304 4234 .773 1.434 .371 .52
5 401 309 190 87 211 222 409 297 191 89 219 210 0 0 125 143 45 30 86 92 78 82 433 429 .95 1.052 .959 1.159 1.211 2.347 52 279 1.103 .74 90 2340 8530 168 177 97 106 0 260 73 187 .884 250 176 1.131 .806 -.178 -.312
6 291 213 188 85 103 128 297 197 192 88 109 112 0 0 60 67 36 33 88 98 65 82 231 221 .805 1.243 1.028 1.328 1.297 2.071 52 293 1.182 .53 90 2470 8540 169 178 110 119 0 179 71 108 1.044 166 94 .958 .863 .063 -.212
7 775 901 197 83 578 818 835 966 198 87 638 883 0 0 343 402 38 34 97 98 90 97 1396 1521 .707 1.415 1.384 1.551 1.346 2.604 80 340 1.426 .81 100 2620 8540 169 179 125 135 0 757 70 687 1.189 812 742 .841 1.163 .25 .218
8 5087 5967 195 87 4892 5880 5213 5883 199 90 5018 5796 0 0 2833 3543 50 29 100 100 100 100 10772 10814 .832 1.202 1.155 1.132 1.238 2.819 80 303 1.246 .89 100 2770 8540 169 179 140 150 0 5014 73 4941 1.01 4944 4871 .99 .971 .014 -.043
9 848 582 202 89 646 493 790 540 206 95 588 451 0 0 460 341 49 34 96 97 85 93 1139 1039 1.31 .763 .767 .812 .752 2.926 80 328 .722 .86 100 2920 8540 169 179 155 165 0 489 75 414 .641 454 379 1.559 .645 -.641 -.634
10 265 138 203 88 62 50 265 129 206 92 62 41 0 0 54 51 41 35 67 56 37 33 112 103 1.24 .806 .661 .68 .875 3.259 80 312 .647 .33 100 3060 8530 168 178 169 179 -50 116 74 42 .678 108 34 1.476 .556 -.561 -.848
11 1880 1338 207 90 1673 1248 2037 1455 210 95 1830 1365 0 0 741 559 42 32 100 100 99 98 2921 3195 1.341 .746 .746 .737 .71 2.002 120 462 .727 .91 120 3200 8530 167 179 182 194 0 1124 76 1049 .627 1223 1147 1.595 .627 -.674 -.674
12 1247 831 215 91 1032 740 1376 768 219 96 1161 677 0 0 678 427 44 33 96 98 90 96 1772 1838 1.395 .717 .583 .798 .704 2.33 52 276 .665 .91 90 3350 8530 168 177 198 207 0 698 76 622 .603 645 569 1.66 .49 -.731 -1.029
13 817 595 223 93 594 502 875 597 225 97 652 504 0 0 384 252 44 34 90 96 84 94 1096 1156 1.183 .845 .773 .919 .783 2.377 52 264 .75 .86 80 3490 8530 169 177 213 221 0 500 78 422 .71 502 424 1.408 .65 -.494 -.622
14 356 362 215 95 141 267 352 354 215 102 137 259 0 0 68 144 39 39 90 96 87 93 408 396 .528 1.894 1.891 1.907 2.036 1.673 32 196 2.145 .7 70 3650 8530 169 176 229 236 0 304 80 224 1.591 297 218 .628 1.589 .67 .668
15 3449 3201 206 95 3243 3106 3681 3229 211 99 3475 3134 0 0 1794 1697 53 39 100 100 97 100 6349 6609 1.044 .958 .902 1.086 .934 2.29 80 303 .946 .86 100 3790 8540 169 179 242 252 0 2690 80 2610 .805 2713 2634 1.242 .758 -.313 -.4
16 1608 2102 207 97 1401 2005 1705 2225 225 107 1498 2128 0 0 688 876 109 79 98 100 90 100 3406 3626 .699 1.431 1.421 1.55 1.396 2.025 52 269 1.459 .87 90 3920 8530 168 177 255 264 0 1766 82 1685 1.203 1870 1788 .832 1.194 .266 .255
17 409 257 200 89 209 168 284 226 214 98 84 137 0 0 662 145 102 69 40 92 11 50 377 221 1.244 .804 1.631 1.443 1.528 2.44 52 272 .224 .74 80 4080 8530 169 177 272 280 0 216 75 141 .675 190 115 1.48 1.371 -.566 .455
18 277 137 199 95 78 42 276 128 208 101 77 33 0 0 53 67 71 44 51 42 11 16 120 110 1.857 .538 .429 .723 .753 2.81 80 353 .807 .52 100 4230 8520 167 177 286 296 -50 115 80 35 .452 108 28 2.21 .36 -1.144 -1.473
19 1227 1326 210 97 1017 1229 1237 1306 224 113 1027 1209 0 0 277 347 119 145 100 100 100 98 2246 2236 .828 1.208 1.177 1.191 1.204 1.447 80 435 1.219 .91 110 4370 8530 167 178 299 310 0 1114 82 1033 1.016 1097 1016 .985 .989 .022 -.016
20 306 183 215 100 91 83 310 186 229 111 95 86 0 0 50 61 132 97 15 43 0 3 174 181 1.096 .912 .905 .785 .874 2.685 32 200 1.043 .46 70 4520 8540 170 177 316 323 0 154 84 70 .766 156 72 1.305 .761 -.384 -.395

Total number of rows: 43008

Table truncated, full table size 9270 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap