NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM91923 Query DataSets for GSM91923
Status Public on Jan 12, 2006
Title MDA2AvsCRG
Sample type RNA
 
Channel 1
Source name CRG mRNA
Organism Homo sapiens
Characteristics CRG mRNA
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name MDA2A total RNA
Organism Homo sapiens
Characteristics MDA2A total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: prostate cancer, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35457.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 Jan 11, 2006
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
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 GPL3341
Series (2)
GSE4016 Gene expression variations in prostate cancer cell lines
GSE4396 Genome-wide characterization of gene expression variations and DNA copy number changes in prostate cancer cell lines

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 same as UNF_VALUE but with flagged values removed
UNF_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 UNF_VALUE
1 1279 322 229 141 1050 181 1350 318 240 149 1121 177 0 0 357 102 86 78 100 81 100 65 1231 1298 5.801 .172 .158 .155 .17 2.008 32 186 .169 .73 70 1610 9280 28 35 25 32 0 325 142 183 .174 321 179 5.743 .159 -2.522 -2.648 -2.648
2 7269 14851 227 134 7042 14717 7563 16293 245 140 7336 16159 0 0 2129 4433 255 69 98 100 98 100 21759 23495 .478 2.09 2.203 2.144 2.101 1.316 52 317 2.16 .96 90 1760 9270 26 35 39 48 0 15001 135 14866 2.111 16458 16322 .474 2.225 1.078 1.154 1.154
3 4189 1625 218 124 3971 1501 4074 1245 249 131 3856 1121 0 0 2254 895 314 60 100 100 96 100 5472 4977 2.646 .378 .291 .39 .36 1.645 32 204 .364 .93 70 1900 9270 27 34 54 61 0 1641 125 1516 .382 1258 1132 2.619 .294 -1.389 -1.768 -1.768
4 1637 857 217 126 1420 731 1472 822 223 133 1255 696 0 0 635 305 68 55 100 100 100 100 2151 1951 1.943 .515 .555 .531 .536 1.471 32 196 .479 .87 70 2050 9270 27 34 69 76 0 866 127 738 .52 830 703 1.923 .56 -.943 -.836 -.836
5 2403 1444 216 126 2187 1318 2256 1349 227 134 2040 1223 0 0 1389 688 74 57 98 100 97 100 3505 3263 1.659 .603 .6 .688 .648 1.767 80 385 .535 .91 100 2190 9270 26 36 82 92 0 1459 127 1331 .609 1363 1235 1.643 .606 -.716 -.724 -.724
6 1700 270 223 125 1477 145 1591 219 234 133 1368 94 0 0 443 131 70 59 100 71 100 46 1622 1462 10.186 .098 .069 .087 .087 2.366 32 207 .1 .59 70 2340 9260 26 33 98 105 0 273 126 146 .099 221 95 10.084 .069 -3.334 -3.849 -3.849
7 3593 2322 221 132 3372 2190 3791 2240 224 135 3570 2108 0 0 1276 1040 64 58 100 100 100 100 5562 5678 1.54 .649 .59 .617 .605 1.618 52 265 .661 .92 80 2490 9270 27 35 113 121 0 2345 133 2212 .656 2263 2129 1.524 .596 -.608 -.746 -.746
8 2301 462 210 128 2091 334 2359 424 222 130 2149 296 0 0 766 196 79 57 100 94 100 94 2425 2445 6.26 .16 .138 .149 .165 1.953 52 248 .15 .82 80 2630 9270 27 35 127 135 0 467 129 337 .161 428 299 6.198 .139 -2.632 -2.845 -2.845
9 1389 389 206 127 1183 262 1410 368 219 133 1204 241 0 0 434 152 73 59 98 92 98 83 1445 1445 4.515 .221 .2 .195 .224 1.999 80 359 .209 .77 100 2780 9270 26 36 141 151 0 393 128 265 .224 372 243 4.47 .202 -2.16 -2.306 -2.306
10 1165 324 215 131 950 193 1092 323 223 138 877 192 0 0 425 124 72 58 100 87 100 68 1143 1069 4.922 .203 .219 .174 .185 2.479 32 146 .167 .66 60 2920 9270 28 34 157 163 0 327 132 195 .205 326 194 4.873 .221 -2.285 -2.177 -2.177
11 5732 758 214 136 5518 622 5815 774 219 141 5601 638 0 0 2131 350 67 57 100 96 100 90 6140 6239 8.871 .113 .114 .103 .112 1.786 80 353 .11 .89 100 3070 9270 26 36 170 180 0 766 137 628 .114 782 644 8.783 .115 -3.135 -3.12 -3.12
12 6363 6568 214 139 6149 6429 6429 7045 243 160 6215 6906 0 0 4570 3855 217 115 96 98 90 98 12578 13121 .956 1.046 1.111 1.26 1.154 1.743 52 220 .923 .94 80 3200 9270 27 35 184 192 0 6634 140 6494 1.056 7116 6976 .947 1.122 .079 .167 .167
13 2167 1559 222 131 1945 1428 2150 1492 247 148 1928 1361 0 0 811 558 182 98 100 100 100 100 3373 3289 1.362 .734 .706 .75 .725 1.432 80 363 .692 .92 100 3360 9270 26 36 199 209 0 1575 132 1442 .742 1507 1375 1.348 .713 -.431 -.488 -.488
14 976 315 223 138 753 177 953 265 231 147 730 127 0 0 361 137 78 60 100 75 100 50 930 857 4.254 .235 .174 .19 .185 2.176 52 289 .107 .48 90 3510 9270 26 35 214 223 0 318 139 179 .237 268 128 4.212 .176 -2.074 -2.509 -2.509
15 2958 374 227 138 2731 236 3015 327 234 150 2788 189 0 0 831 146 73 64 98 88 98 77 2967 2977 11.572 .086 .068 .08 .082 1.85 80 324 .085 .78 100 3660 9270 26 36 229 239 0 378 139 238 .087 330 191 11.456 .068 -3.518 -3.868 -3.868
16 15978 16837 224 134 15754 16703 16039 17175 237 146 15815 17041 0 0 5713 6806 86 70 100 100 100 100 32457 32856 .943 1.06 1.078 1.053 1.058 1.591 80 338 1.084 .95 100 3800 9270 26 36 243 253 0 17007 135 16872 1.071 17348 17213 .934 1.088 .099 .122 .122
17 5455 2376 221 136 5234 2240 5483 2279 230 145 5262 2143 0 0 1531 804 87 64 100 100 100 100 7474 7405 2.337 .428 .407 .418 .425 1.464 52 254 .421 .93 80 3950 9260 26 34 259 267 0 2400 137 2263 .432 2302 2165 2.313 .411 -1.21 -1.281 -1.281
18 344 155 231 137 113 18 246 144 235 144 15 7 0 0 317 66 70 60 28 25 19 3 131 22 6.278 .159 .467 .615 .583 5.153 52 235 .132 .37 80 4100 9250 25 33 274 282 -50 157 138 18 .161 145 7 6.215 .471 -2.636 -1.085
19 5569 8413 225 145 5344 8268 5717 8530 260 158 5492 8385 0 0 1767 2891 500 102 98 100 98 100 13612 13877 .646 1.547 1.527 1.558 1.559 1.604 80 382 1.583 .92 110 4240 9260 24 35 286 297 0 8498 146 8352 1.563 8616 8470 .64 1.542 .644 .625 .625
20 3318 3062 217 145 3101 2917 3549 3313 258 159 3332 3168 0 0 1272 1116 528 106 95 98 91 98 6018 6500 1.063 .941 .951 .945 .929 1.595 80 343 .855 .88 100 4390 9260 25 35 302 312 0 3093 146 2946 .95 3346 3200 1.052 .96 -.074 -.058 -.058

Total number of rows: 43104

Table truncated, full table size 9778 Kbytes.




Supplementary data files not provided

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap