NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM82121 Query DataSets for GSM82121
Status Public on Nov 05, 2005
Title actA TC1 T60
Sample type RNA
 
Channel 1
Source name CRE reference pool
Organism Homo sapiens
Characteristics CRE reference pool
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name experimental sample
Organism Homo sapiens
Characteristics experimental sample
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Pathogen, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/8089.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Nov 04, 2005
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 GPL2948
Series (1)
GSE3567 Listeria infection of Caco-2 cells

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 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
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

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
1 3449 3954 169 143 3280 3811 null null 349 296 null null null null null null null null 96 100 null null null null .861 1.162 null null 1.169 null 80 409 1.189 .95 null null null 71 81 126 136 0 6083 220 5863 1.788 null null .559 null .838 null
2 3050 2311 150 134 2900 2177 null null 288 237 null null null null null null null null 92 90 null null null null 1.332 .751 null null .746 null 120 422 .707 .95 null null null 71 83 142 154 0 3555 206 3349 1.155 null null .866 null .208 null
3 2209 2448 160 144 2049 2304 null null 325 285 null null null null null null null null 97 92 null null null null .889 1.124 null null 1.158 null 80 340 1.104 .94 null null null 71 82 156 167 0 3766 221 3545 1.73 null null .578 null .791 null
4 1971 1290 418 408 1553 882 null null 573 561 null null null null null null null null 78 65 null null null null 1.761 .568 null null .569 null 80 330 .598 .82 null null null 70 80 172 182 0 1984 627 1357 .874 null null 1.144 null -.195 null
5 6687 8214 148 147 6539 8067 null null 376 355 null null null null null null null null 100 100 null null null null .811 1.234 null null 1.215 null 156 559 1.224 .96 null null null 69 83 186 200 0 12636 226 12410 1.898 null null .527 null .924 null
6 2460 1691 146 140 2314 1551 null null 245 195 null null null null null null null null 87 85 null null null null 1.492 .67 null null .663 null 120 365 .649 .94 null null null 71 83 201 213 0 2601 215 2386 1.031 null null .97 null .044 null
7 1464 1143 148 140 1316 1003 null null 232 189 null null null null null null null null 86 85 null null null null 1.312 .762 null null .729 null 80 313 .731 .92 null null null 72 82 217 227 0 1758 215 1543 1.172 null null .853 null .23 null
8 1557 1716 149 138 1408 1578 null null 155 141 null null null null null null null null 91 97 null null null null .892 1.121 null null 1.107 null 80 316 1.038 .92 null null null 73 83 232 242 0 2640 212 2428 1.724 null null .58 null .786 null
9 15165 7834 159 141 15006 7693 null null 202 164 null null null null null null null null 100 100 null null null null 1.951 .513 null null .519 null 80 323 .502 .93 null null null 73 83 247 257 0 12052 216 11836 .789 null null 1.268 null -.342 null
10 1086 587 169 142 917 445 null null 208 164 null null null null null null null null 90 83 null null null null 2.061 .485 null null .444 null 80 319 .521 .88 null null null 73 83 262 272 0 903 218 685 .747 null null 1.339 null -.421 null
11 1651 622 169 148 1482 474 null null 179 153 null null null null null null null null 97 86 null null null null 3.127 .32 null null .324 null 80 307 .315 .89 null null null 73 83 276 286 0 956 227 729 .492 null null 2.033 null -1.024 null
12 7123 10985 157 137 6966 10848 null null 164 143 null null null null null null null null 97 98 null null null null .642 1.557 null null 1.548 null 80 307 1.527 .94 null null null 74 84 290 300 0 16900 210 16690 2.396 null null .417 null 1.261 null
13 10996 7470 170 142 10826 7328 null null 2388 1609 null null null null null null null null 96 92 null null null null 1.477 .677 null null .692 null 80 330 .653 .9 null null null 74 84 305 315 -100 11492 218 11274 1.041 null null .96 null .058 null
14 22939 15162 281 225 22658 14937 null null 4346 3089 null null null null null null null null 98 100 null null null null 1.517 .659 null null .665 null 80 372 .617 .88 null null null 74 84 320 330 -100 23326 346 22980 1.014 null null .986 null .02 null
15 2370 1475 179 166 2191 1309 null null 1681 1374 null null null null null null null null 0 0 null null null null 1.674 .597 null null .609 null 80 334 .619 .81 null null null 73 83 336 346 0 2269 255 2014 .919 null null 1.088 null -.122 null
16 3809 1421 179 170 3630 1251 null null 198 184 null null null null null null null null 92 86 null null null null 2.902 .345 null null .355 null 80 338 .346 .93 null null null 72 83 349 360 0 2186 261 1925 .53 null null 1.886 null -.915 null
17 12944 15037 183 170 12761 14867 null null 194 181 null null null null null null null null 98 95 null null null null .858 1.165 null null 1.176 null 120 440 1.188 .96 null null null 72 84 364 376 0 23133 261 22872 1.792 null null .558 null .842 null
18 234 231 179 166 55 65 null null 182 171 null null null null null null null null 41 46 null null null null .846 1.182 null null 1.038 null 80 323 .503 .49 null null null 75 85 380 390 0 355 255 100 1.818 null null .55 null .862 null
19 6448 4781 176 167 6272 4614 null null 179 174 null null null null null null null null 96 92 null null null null 1.359 .736 null null .744 null 80 353 .729 .93 null null null 74 84 395 405 0 7355 256 7099 1.132 null null .884 null .179 null
20 3950 3615 170 173 3780 3442 null null 177 178 null null null null null null null null 100 100 null null null null 1.098 .911 null null .91 null 52 294 .863 .94 null null null 75 84 410 419 0 5561 266 5295 1.401 null null .714 null .486 null

Total number of rows: 24192

Table truncated, full table size 5748 Kbytes.




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