NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM71881 Query DataSets for GSM71881
Status Public on Aug 26, 2005
Title 300p-8 2C-N vs 2C-S
Sample type genomic
 
Channel 1
Source name 300p-8 2C-S
Organism Helicobacter pylori
Characteristics 300p-8 2C-S
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name 300p-8 2C-N
Organism Helicobacter pylori
Characteristics 300p-8 2C-N
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24521.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 2510 1085 176 258 2334 827 2318 1030 179 257 2142 772 0 0 1306 511 32 41 100 96 100 90 3161 2914 2.822 .354 .36 .356 .336 2.769 52 332 .325 .85 80 1240 40980 101 109 85 93 0 2047 487 1560 .669 1943 1457 1.496 .68 -.581 -.556
2 729 376 170 255 559 121 601 351 173 261 431 96 0 0 346 94 25 44 100 78 100 53 680 527 4.62 .216 .223 .223 .211 2.059 32 160 .176 .66 60 1480 40950 99 105 110 116 0 709 481 228 .408 662 181 2.449 .42 -1.292 -1.251
3 486 1628 178 281 308 1347 425 1462 179 285 247 1181 0 0 218 751 25 51 90 100 84 100 1655 1428 .229 4.373 4.781 5.072 5.448 2.976 32 236 5.258 .74 70 1730 40970 100 107 134 141 0 3072 530 2542 8.252 2758 2228 .121 9.021 3.045 3.173
4 191 301 173 285 18 16 167 286 175 287 -6 1 0 0 84 75 25 48 21 20 13 6 34 -5 1.125 .889 null 1.059 1 3.663 80 552 1.638 .3 100 1950 40960 98 108 155 165 -50 568 538 30 1.677 540 2 .596 null .746 null
5 177 278 175 282 2 -4 174 270 176 283 -1 -12 0 0 38 49 24 46 22 15 8 3 -2 -13 null null null 1.449 1.45 2.438 80 552 19.066 .05 100 2190 40960 98 108 179 189 -50 525 532 -8 null 509 null null null null null
6 222 365 172 284 50 81 185 334 174 287 13 50 0 0 108 124 27 48 36 51 20 26 131 63 .617 1.62 3.846 1.991 1.595 3.854 80 552 1.78 .47 100 2430 40960 98 108 203 213 -100 689 536 153 3.057 630 94 .327 7.257 1.612 2.859
7 490 402 174 302 316 100 484 391 175 304 310 89 0 0 81 101 25 44 100 75 100 50 416 399 3.16 .316 .287 .24 .334 3.513 12 98 .356 .43 50 2670 40950 99 104 229 234 0 758 570 189 .597 738 168 1.675 .542 -.744 -.884
8 509 564 154 276 355 288 508 542 160 279 354 266 0 0 154 102 36 48 100 100 100 100 643 620 1.233 .811 .751 .863 .763 2.131 12 104 .783 .72 50 2900 40960 100 105 252 257 0 1064 521 543 1.531 1023 502 .653 1.418 .614 .504
9 1475 542 153 285 1322 257 1569 559 157 287 1416 274 0 0 457 112 24 46 100 96 100 96 1579 1690 5.144 .194 .194 .184 .21 1.488 32 233 .191 .83 70 3160 40950 98 105 277 284 0 1023 538 485 .367 1055 517 2.726 .365 -1.447 -1.454
10 235 337 155 291 80 46 195 313 158 292 40 22 0 0 133 107 21 50 63 33 48 16 126 62 1.739 .575 .55 1.294 1.167 4.262 80 552 .897 .59 100 3390 40950 97 107 299 309 -50 636 549 87 1.085 591 42 .922 1.038 .118 .053
11 323 1159 157 303 166 856 201 447 159 304 44 144 0 0 302 1707 21 48 63 75 50 62 1022 188 .194 5.157 3.273 3.255 3.296 3.959 80 552 6.874 .8 100 3630 40950 97 107 323 333 -100 2187 572 1615 9.729 843 272 .103 6.175 3.282 2.626
12 720 421 172 322 548 99 686 396 184 438 514 74 0 0 173 106 64 1339 100 0 100 0 647 588 5.535 .181 .144 .172 .166 2.214 32 230 .251 .57 70 3880 40940 97 104 349 356 0 794 608 187 .341 747 140 2.934 .272 -1.553 -1.88
13 1137 1637 186 332 951 1305 1254 1754 205 332 1068 1422 0 0 469 705 63 49 92 88 90 88 2256 2490 .729 1.372 1.331 1.276 1.387 2.978 52 332 1.521 .84 80 4110 40950 98 106 372 380 0 3089 626 2462 2.589 3309 2683 .386 2.512 1.372 1.329
14 669 883 186 348 483 535 489 803 193 354 303 455 0 0 388 220 32 52 96 100 90 100 1018 758 .903 1.108 1.502 1.533 1.253 2.572 32 236 .877 .78 70 4370 40960 99 106 398 405 0 1666 657 1009 2.09 1515 858 .478 2.833 1.063 1.502
15 672 732 185 368 487 364 731 721 183 373 546 353 0 0 219 135 27 54 100 100 100 100 851 899 1.338 .747 .647 .805 .736 1.994 32 170 .732 .77 60 4590 40950 99 105 421 427 0 1381 694 687 1.41 1360 666 .709 1.22 .496 .287
16 240 396 177 368 63 28 193 370 179 372 16 2 0 0 130 115 21 60 45 23 30 11 91 18 2.25 .444 .125 1.275 1.268 2.747 80 538 1.118 .53 100 4830 40940 96 106 443 453 -50 747 694 53 .839 698 4 1.193 .236 -.254 -2.084
17 287 425 176 372 111 53 200 378 177 373 24 6 0 0 229 186 22 54 51 27 32 17 164 30 2.094 .477 .25 1.818 1.658 3.153 80 538 .778 .62 100 5070 40940 96 106 467 477 -50 802 702 100 .901 713 11 1.11 .472 -.151 -1.084
18 14814 702 216 262 14598 440 15293 645 272 272 15077 383 0 0 6437 300 277 57 100 87 100 81 15038 15460 33.177 .03 .025 .031 .03 1.379 32 220 .031 .84 70 1220 41200 123 130 83 90 0 1325 494 830 .057 1217 723 17.584 .048 -4.136 -4.383
19 603 824 210 286 393 538 579 841 219 288 369 555 0 0 239 171 46 46 96 100 93 100 931 924 .73 1.369 1.504 1.629 1.416 2.342 32 176 1.287 .76 60 1470 41200 124 130 109 115 0 1555 540 1015 2.583 1587 1047 .387 2.838 1.369 1.505
20 260 315 193 289 67 26 218 293 194 290 25 4 0 0 145 80 26 48 46 31 26 12 93 29 2.577 .388 .16 1.041 .882 4.003 80 560 .375 .27 100 1720 41200 122 132 132 142 -100 594 545 49 .732 553 8 1.366 .302 -.45 -1.728

Total number of rows: 4608

Table truncated, full table size 1026 Kbytes.




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