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Sample GSM78787 Query DataSets for GSM78787
Status Public on Oct 20, 2005
Title M1.16 genomic vs Tigr/Astra Ref 4
Sample type genomic
 
Channel 1
Source name 1ug Tigr genomic DNA + 1 ug Astra genomic DNA
Organism Helicobacter pylori
Characteristics 1ug Tigr genomic DNA + 1 ug Astra genomic DNA
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name 2 ug M1.16 genomic
Organism Helicobacter pylori
Characteristics 2 ug M1.16 genomic
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7914.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 Oct 19, 2005
Last update date Feb 20, 2008
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 GPL15
Series (1)
GSE3479 Helicobacter pylori bacterial populations

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 LOG_RAT2N_MEDIANs 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 LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized LOG_RAT2N_MEDIAN 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 LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized LOG_RAT2N_MEDIAN 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 same as UNF_VALUE but with flagged values removed
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
UNF_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

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 UNF_VALUE
1 4416 6480 216 242 4200 6238 null null 226 252 null null null null null null null null 100 98 null null null null .673 1.485 null null 1.427 null 80 552 1.453 .97 null null null 86 96 94 104 0 5586 208 5378 1.28 null null .781 null .357 null .357
2 3428 1164 208 238 3220 926 null null 215 244 null null null null null null null null 95 88 null null null null 3.477 .288 null null .293 null 80 656 .28 .96 null null null 85 96 117 128 0 1003 205 798 .248 null null 4.035 null -2.013 null -2.013
3 1302 1872 214 243 1088 1629 null null 221 249 null null null null null null null null 96 96 null null null null .668 1.497 null null 1.477 null 80 554 1.461 .97 null null null 86 96 143 153 0 1613 209 1404 1.29 null null .775 null .368 null .368
4 222 251 206 237 16 14 null null 211 246 null null null null null null null null 16 20 null null null null 1.143 .875 null null .867 null 120 781 .148 .11 null null null 83 95 165 177 0 216 204 12 .75 null null 1.333 null -.415 null -.415
5 211 261 193 235 18 26 null null 195 238 null null null null null null null null 30 26 null null null null .692 1.444 null null 1.317 null 120 794 .087 .05 null null null 83 95 189 201 0 225 202 23 1.278 null null .783 null .354 null .354
6 1188 545 199 246 989 299 null null 198 248 null null null null null null null null 100 90 null null null null 3.308 .302 null null .319 null 32 176 .285 .91 null null null 88 94 217 223 0 469 212 257 .26 null null 3.848 null -1.944 null -1.944
7 431 443 192 233 239 210 null null 194 234 null null null null null null null null 96 80 null null null null 1.138 .879 null null .948 null 52 340 .744 .81 null null null 87 95 240 248 0 381 200 181 .757 null null 1.32 null -.401 null -.401
8 348 362 200 226 148 136 null null 201 230 null null null null null null null null 75 71 null null null null 1.088 .919 null null .985 null 52 340 .681 .7 null null null 86 94 263 271 0 312 194 118 .797 null null 1.254 null -.327 null -.327
9 1919 2285 205 223 1714 2062 null null 219 244 null null null null null null null null 97 95 null null null null .831 1.203 null null 1.222 null 80 656 1.173 .96 null null null 85 96 285 296 0 1969 192 1777 1.037 null null .965 null .052 null .052
10 336 380 200 216 136 164 null null 200 216 null null null null null null null null 81 81 null null null null .829 1.206 null null 1.502 null 32 236 .647 .61 null null null 87 94 313 320 0 327 186 141 1.037 null null .965 null .052 null .052
11 550 634 210 211 340 423 null null 212 224 null null null null null null null null 84 93 null null null null .804 1.244 null null 1.47 null 32 176 .933 .88 null null null 89 95 336 342 0 546 181 365 1.074 null null .932 null .102 null .102
12 1666 3391 217 234 1449 3157 null null 221 241 null null null null null null null null 96 100 null null null null .459 2.179 null null 2.195 null 156 1064 2.07 .97 null null null 85 99 356 370 0 2923 201 2722 1.879 null null .532 null .91 null .91
13 1320 1049 224 255 1096 794 null null 230 262 null null null null null null null null 93 87 null null null null 1.38 .724 null null .741 null 80 650 .708 .94 null null null 87 98 381 392 0 904 219 685 .625 null null 1.6 null -.678 null -.678
14 1606 2279 222 258 1384 2021 null null 226 264 null null null null null null null null 98 98 null null null null .685 1.46 null null 1.472 null 52 340 1.391 .98 null null null 87 95 408 416 0 1964 222 1742 1.259 null null .794 null .332 null .332
15 587 862 219 259 368 603 null null 222 266 null null null null null null null null 95 99 null null null null .61 1.639 null null 1.764 null 120 820 1.315 .89 null null null 85 97 430 442 0 743 223 520 1.413 null null .708 null .499 null .499
16 529 720 220 261 309 459 null null 225 275 null null null null null null null null 96 96 null null null null .673 1.485 null null 1.434 null 32 236 1.153 .83 null null null 87 94 457 464 0 620 225 395 1.278 null null .782 null .354 null .354
17 896 1098 219 269 677 829 null null 228 280 null null null null null null null null 96 100 null null null null .817 1.225 null null 1.268 null 32 236 1.084 .92 null null null 86 93 480 487 0 946 231 715 1.056 null null .947 null .079 null .079
18 381 480 194 224 187 256 null null 198 229 null null null null null null null null 90 96 null null null null .73 1.369 null null 1.225 null 32 236 1.134 .76 null null null 110 117 97 104 0 413 193 220 1.176 null null .85 null .234 null .234
19 1609 1653 202 227 1407 1426 null null 205 231 null null null null null null null null 100 100 null null null null .987 1.014 null null 1.004 null 32 236 .974 .97 null null null 110 117 120 127 0 1425 195 1230 .874 null null 1.144 null -.194 null -.194
20 224 257 207 238 17 19 null null 214 243 null null null null null null null null 15 18 null null null null .895 1.118 null null 1.203 null 120 791 .372 .38 null null null 107 119 141 153 0 221 205 16 .941 null null 1.063 null -.087 null -.087

Total number of rows: 4608

Table truncated, full table size 1145 Kbytes.




Supplementary data files not provided

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