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Sample GSM82133 Query DataSets for GSM82133
Status Public on Nov 05, 2005
Title actA TC1 T120
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/2000-07/8090.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
1 479 374 202 72 277 302 null null 419 131 null null null null null null null null 0 80 null null null null .917 1.09 null null 1.187 null 52 326 .223 .83 null null null 89 98 94 103 0 705 135 570 2.058 null null .486 null 1.041 null
2 634 272 209 74 425 198 null null 439 133 null null null null null null null null 0 43 null null null null 2.146 .466 null null .518 null 80 342 .057 .47 null null null 89 99 110 120 0 513 139 374 .88 null null 1.136 null -.184 null
3 484 252 219 73 265 179 null null 277 87 null null null null null null null null 48 82 null null null null 1.48 .675 null null .926 null 80 402 .186 .53 null null null 88 99 124 135 0 475 137 338 1.275 null null .784 null .351 null
4 325 103 207 71 118 32 null null 279 82 null null null null null null null null 3 26 null null null null 3.688 .271 null null .311 null 80 351 .069 .41 null null null 90 100 140 150 0 194 133 61 .517 null null 1.934 null -.952 null
5 974 834 232 77 742 757 null null 333 130 null null null null null null null null 87 95 null null null null .98 1.02 null null 1.033 null 80 397 .652 .75 null null null 90 101 155 166 0 1573 145 1428 1.925 null null .52 null .945 null
6 796 537 229 77 567 460 null null 337 129 null null null null null null null null 85 100 null null null null 1.233 .811 null null .855 null 80 406 .463 .68 null null null 89 100 170 181 0 1013 145 868 1.531 null null .653 null .614 null
7 462 178 200 66 262 112 null null 252 72 null null null null null null null null 47 81 null null null null 2.339 .427 null null .59 null 80 306 .124 .47 null null null 91 101 186 196 0 335 124 211 .805 null null 1.242 null -.312 null
8 373 174 196 67 177 107 null null 256 73 null null null null null null null null 13 70 null null null null 1.654 .605 null null 1.048 null 80 308 .087 .33 null null null 91 101 200 210 0 328 126 202 1.141 null null .876 null .191 null
9 1788 700 189 67 1599 633 null null 247 74 null null null null null null null null 87 86 null null null null 2.526 .396 null null .427 null 80 352 .382 .89 null null null 90 100 215 225 0 1320 126 1194 .747 null null 1.339 null -.421 null
10 234 73 187 66 47 7 null null 235 74 null null null null null null null null 2 5 null null null null 6.714 .149 null null .295 null 80 337 .128 .8 null null null 91 101 230 240 0 137 124 13 .277 null null 3.615 null -1.854 null
11 324 91 193 66 131 25 null null 253 76 null null null null null null null null 15 15 null null null null 5.24 .191 null null .217 null 80 384 .076 .45 null null null 91 101 245 255 0 171 124 47 .359 null null 2.787 null -1.479 null
12 830 1367 196 67 634 1300 null null 267 75 null null null null null null null null 82 90 null null null null .488 2.05 null null 2.261 null 80 339 1.083 .64 null null null 90 100 261 271 0 2579 126 2453 3.869 null null .258 null 1.952 null
13 600 257 195 66 405 191 null null 252 72 null null null null null null null null 81 83 null null null null 2.12 .472 null null .492 null 80 390 .22 .6 null null null 90 101 274 285 0 484 124 360 .889 null null 1.125 null -.17 null
14 2073 1051 222 74 1851 977 null null 705 319 null null null null null null null null 100 92 null null null null 1.895 .528 null null .547 null 80 375 .503 .91 null null null 92 102 291 301 0 1983 139 1844 .996 null null 1.004 null -.005 null
15 1274 674 223 75 1051 599 null null 703 320 null null null null null null null null 55 67 null null null null 1.755 .57 null null .599 null 80 357 .496 .89 null null null 92 102 306 316 0 1271 141 1130 1.075 null null .93 null .105 null
16 655 219 193 67 462 152 null null 246 77 null null null null null null null null 88 80 null null null null 3.039 .329 null null .361 null 80 349 .282 .76 null null null 91 101 322 332 0 413 126 287 .621 null null 1.61 null -.687 null
17 1481 1559 201 67 1280 1492 null null 254 93 null null null null null null null null 95 90 null null null null .858 1.166 null null 1.191 null 80 381 1.14 .92 null null null 90 101 335 346 0 2941 126 2815 2.199 null null .455 null 1.137 null
18 258 73 203 66 55 7 null null 265 95 null null null null null null null null 6 0 null null null null 7.857 .127 null null .186 null 80 354 .24 .27 null null null 92 102 351 361 0 137 124 13 .236 null null 4.231 null -2.081 null
19 1117 780 202 66 915 714 null null 257 71 null null null null null null null null 98 100 null null null null 1.282 .78 null null .807 null 80 416 .634 .84 null null null 90 101 366 377 0 1471 124 1347 1.472 null null .679 null .558 null
20 431 234 206 67 225 167 null null 252 72 null null null null null null null null 65 90 null null null null 1.347 .742 null null .796 null 52 308 .243 .53 null null null 90 99 381 390 0 441 126 315 1.4 null null .714 null .485 null

Total number of rows: 24192

Table truncated, full table size 5771 Kbytes.




Supplementary data files not provided
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