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Sample GSM71883 Query DataSets for GSM71883
Status Public on Aug 26, 2005
Title 300p-10 2C-N vs 2C-S
Sample type genomic
 
Channel 1
Source name 300p-10 2C-S
Organism Helicobacter pylori
Characteristics 300p-10 2C-S
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name 300p-10 2C-N
Organism Helicobacter pylori
Characteristics 300p-10 2C-N
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24523.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 Aug 25, 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 GPL15
Series (1)
GSE3197 MATT mapping of Transposon insertions sites of strain G27 GPS-cat library

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 4286 862 146 654 4140 208 4106 850 152 675 3960 196 0 0 1518 236 37 197 100 50 100 18 4348 4156 19.904 .05 .049 .064 .065 2.104 32 176 .047 .4 60 1210 13020 123 129 98 104 0 2535 1924 612 .148 2500 576 6.767 .146 -2.759 -2.78
2 490 705 155 648 335 57 177 688 161 659 22 40 0 0 757 214 37 203 42 22 32 5 392 62 5.877 .17 1.818 1.657 2.118 6.638 80 552 .157 .27 100 1420 13010 120 130 117 127 -100 2074 1906 168 .5 2024 118 1.998 5.348 -.999 2.419
3 295 738 180 653 115 85 189 726 185 664 9 73 0 0 279 212 49 204 30 26 20 8 200 82 1.353 .739 8.111 2.26 1.753 5.646 80 552 2.984 .22 100 1660 13010 120 130 141 151 -50 2171 1921 250 2.174 2135 215 .46 23.856 1.12 4.576
4 232 654 177 645 55 9 162 648 185 654 -15 3 0 0 224 188 49 206 15 13 11 5 64 -12 6.111 .164 null 2.755 3.155 5.064 80 552 10.403 .11 100 1900 13010 120 130 165 175 -100 1924 1897 26 .481 1906 9 2.078 null -1.055 null
5 220 614 162 653 58 -39 143 575 181 661 -19 -78 0 0 244 208 71 212 11 15 10 0 19 -97 null null null 4.433 4.667 4.018 80 552 3.907 .29 100 2140 13010 120 130 189 199 -100 1806 1921 -115 null 1691 null null null null null
6 369 712 202 651 167 61 238 711 217 666 36 60 0 0 407 211 77 198 26 20 15 3 228 96 2.738 .365 1.667 1.82 2.139 4.594 80 552 .406 .13 100 2380 13010 120 130 213 223 -100 2094 1915 179 1.074 2091 176 .931 4.902 .103 2.293
7 465 658 168 631 297 27 208 616 192 650 40 -15 0 0 549 218 63 202 42 18 35 5 324 25 11 .091 null 1.391 1.744 6.656 80 538 .151 .13 100 2620 13000 119 129 237 247 -100 1935 1856 79 .267 1812 null 3.74 null -1.903 null
8 542 673 157 617 385 56 191 661 164 633 34 44 0 0 665 198 38 191 47 23 36 5 441 78 6.875 .145 1.294 1.008 1.075 10.052 80 538 .149 .21 100 2860 13000 119 129 261 271 -100 1979 1815 165 .428 1944 129 2.338 3.806 -1.225 1.928
9 16996 958 245 607 16751 351 17381 957 268 605 17136 350 0 0 5712 257 139 190 100 71 100 42 17102 17486 47.724 .021 .02 .03 .028 1.793 52 312 .019 .56 80 3100 12990 119 127 286 294 0 2818 1785 1032 .062 2815 1029 16.226 .06 -4.02 -4.057
10 349 593 208 550 141 43 246 574 212 580 38 24 0 0 312 201 60 193 43 23 23 7 184 62 3.279 .305 .632 1.666 2.002 5.591 80 552 .741 .14 100 3340 13000 119 129 309 319 -100 1744 1618 126 .897 1688 71 1.115 1.858 -.157 .893
11 660 705 220 641 440 64 296 738 223 648 76 97 0 0 786 230 40 194 61 28 48 5 504 173 6.875 .145 1.276 .797 .944 5.952 80 552 .069 .12 100 3580 13000 119 129 333 343 -100 2074 1885 188 .428 2171 285 2.338 3.754 -1.225 1.908
12 456 923 199 721 257 202 468 912 199 710 269 191 0 0 132 228 39 211 96 43 87 18 459 460 1.272 .786 .71 1.146 1.013 3.29 32 220 3.374 .28 70 3830 12980 118 125 359 366 0 2715 2121 594 2.312 2682 562 .433 2.088 1.209 1.062
13 2699 1016 216 652 2483 364 2660 1037 219 685 2444 385 0 0 750 262 41 204 100 68 100 40 2847 2829 6.821 .147 .158 .13 .153 2.327 32 220 .123 .5 70 4080 12980 118 125 384 391 0 2988 1918 1071 .431 3050 1132 2.319 .463 -1.214 -1.11
14 409 779 204 680 205 99 282 766 206 696 78 86 0 0 355 220 47 209 55 27 47 10 304 164 2.071 .483 1.103 1.592 1.95 4.746 80 538 1.554 .19 100 4300 12990 118 128 405 415 -50 2291 2000 291 1.42 2253 253 .704 3.243 .506 1.697
15 968 800 225 688 743 112 1026 854 225 699 801 166 0 0 180 323 75 217 100 41 100 16 855 967 6.634 .151 .207 .382 .428 1.741 12 80 .15 .14 50 4560 12970 118 123 433 438 0 2353 2024 329 .443 2512 488 2.256 .61 -1.173 -.714
16 254 690 163 673 91 17 163 684 186 682 0 11 0 0 244 170 65 203 22 10 15 1 108 11 5.353 .187 null 2.274 3.552 4.662 80 538 5.802 .13 100 4790 12990 118 128 454 464 -100 2029 1979 50 .549 2012 32 1.82 null -.864 null
17 445 676 203 696 242 -20 247 667 204 698 44 -29 0 0 397 187 50 200 47 13 35 0 222 15 null null null 1.282 2.037 6.015 80 538 .265 .09 100 5030 12990 118 128 478 488 -100 1988 2047 -59 null 1962 null null null null null
18 12333 1308 174 679 12159 629 12034 1353 191 661 11860 674 0 0 2517 327 60 184 100 90 100 81 12788 12534 19.331 .052 .057 .047 .056 1.716 32 176 .055 .81 60 1200 13240 145 151 97 103 0 3847 1997 1850 .152 3979 1982 6.572 .167 -2.716 -2.581
19 2722 828 233 667 2489 161 3166 829 237 674 2933 162 0 0 1702 235 43 190 96 42 96 13 2650 3095 15.46 .065 .055 .122 .074 5.579 52 340 .053 .34 80 1440 13240 144 152 120 128 0 2435 1962 474 .19 2438 476 5.256 .162 -2.394 -2.622
20 353 713 219 661 134 52 232 727 221 680 13 66 0 0 307 199 47 205 33 18 25 2 186 79 2.577 .388 5.077 2.304 2.565 5.375 80 538 4.618 .11 100 1660 13250 144 154 141 151 -100 2097 1944 153 1.141 2138 194 .876 14.932 .191 3.9

Total number of rows: 4608

Table truncated, full table size 1025 Kbytes.




Supplementary data files not provided
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