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Sample GSM71871 Query DataSets for GSM71871
Status Public on Aug 26, 2005
Title 300p-13 2A-N vs 2A-S
Sample type genomic
 
Channel 1
Source name 300p-13 2A-S
Organism Helicobacter pylori
Characteristics 300p-13 2A-S
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name 300p-13 2A-N
Organism Helicobacter pylori
Characteristics 300p-13 2A-N
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/23863.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
1 435 1172 107 248 328 924 457 1189 108 254 350 941 0 0 172 316 22 55 92 100 90 100 1252 1291 .355 2.817 2.689 2.821 2.888 1.974 52 320 3.136 .76 80 1290 14160 93 101 85 93 0 1890 400 1490 4.544 1918 1518 .22 4.336 2.184 2.116
2 2830 503 112 264 2718 239 2644 484 120 270 2532 220 0 0 1736 140 35 64 100 92 100 73 2957 2752 11.372 .088 .087 .091 .08 2.861 52 340 .059 .66 80 1510 14140 91 99 107 115 0 811 426 385 .142 781 355 7.051 .14 -2.818 -2.835
3 384 312 116 232 268 80 354 298 117 239 238 66 0 0 168 75 18 55 100 59 96 28 348 304 3.35 .299 .277 .264 .296 2.61 32 176 .296 .53 60 1780 14150 93 99 135 141 0 503 374 129 .481 481 106 2.077 .447 -1.055 -1.161
4 138 271 112 257 26 14 127 269 113 261 15 12 0 0 37 47 18 50 42 22 27 3 40 27 1.857 .538 .8 1.744 1.6 3.795 80 552 20.22 .06 100 2010 14130 89 99 156 166 -50 437 415 23 .868 434 19 1.151 1.29 -.203 .368
5 121 276 116 260 5 16 116 277 118 265 0 17 0 0 33 49 20 51 26 21 12 3 21 17 .313 3.2 null 1.554 1.517 4.09 80 552 17.878 .09 100 2250 14130 89 99 180 190 -50 445 419 26 5.161 447 27 .194 null 2.368 null
6 163 256 124 258 39 -2 137 257 126 260 13 -1 0 0 76 40 22 49 35 12 20 0 37 12 null null null .804 .955 4.88 80 552 .384 .03 100 2490 14130 89 99 204 214 -100 413 416 -3 null 415 null null null null null
7 188 251 130 265 58 -14 156 248 132 264 26 -17 0 0 93 49 23 48 50 10 47 1 44 9 null null null .769 .833 5.025 80 552 .372 .16 100 2730 14130 89 99 228 238 -50 405 427 -23 null 400 null null null null null
8 405 342 113 267 292 75 410 337 116 268 297 70 0 0 83 77 22 46 100 66 100 41 367 367 3.893 .257 .236 .267 .322 2.67 12 90 .356 .4 50 2980 14120 90 95 255 260 0 552 431 121 .414 544 113 2.414 .38 -1.271 -1.395
9 3505 7409 119 237 3386 7172 4068 7625 126 241 3949 7388 0 0 1809 3388 30 53 100 100 100 100 10558 11337 .472 2.118 1.871 2.408 2.024 2.411 52 415 2.299 .84 90 3210 14130 89 98 276 285 0 11950 382 11568 3.416 12298 11916 .293 3.018 1.772 1.593
10 598 738 157 271 441 467 604 736 155 274 447 465 0 0 51 131 30 54 100 100 100 100 908 912 .944 1.059 1.04 1.028 .962 1.35 12 104 1.109 .69 50 3450 14130 91 96 302 307 0 1190 437 753 1.708 1187 750 .585 1.678 .772 .747
11 296 390 203 306 93 84 230 324 209 311 27 18 0 0 170 174 45 55 38 40 31 31 177 45 1.107 .903 .667 1.101 .996 2.714 80 552 1.075 .54 100 3690 14130 89 99 324 334 -50 629 494 135 1.457 523 29 .686 1.075 .543 .105
12 284 251 146 246 138 5 247 238 157 253 101 -8 0 0 173 86 43 63 61 21 52 10 143 93 27.6 .036 null .496 .467 4.775 80 552 .327 .4 100 3930 14130 89 99 348 358 -50 405 397 8 .058 384 null 17.112 null -4.097 null
13 1336 945 146 246 1190 699 1465 1019 153 261 1319 773 0 0 558 347 37 69 96 98 92 94 1889 2092 1.702 .587 .586 .64 .562 3.483 52 320 .536 .79 80 4180 14120 89 97 374 382 0 1524 397 1127 .947 1644 1247 1.056 .945 -.078 -.081
14 588 1031 204 250 384 781 586 1022 212 259 382 772 0 0 186 193 57 76 96 100 90 100 1165 1154 .492 2.034 2.021 2.323 1.97 1.862 32 230 2.052 .84 70 4410 14120 89 96 397 404 0 1663 403 1260 3.28 1648 1245 .305 3.26 1.714 1.705
15 577 537 249 370 328 167 641 544 260 373 392 174 0 0 190 139 106 71 84 81 71 65 495 566 1.964 .509 .444 .463 .522 2.584 32 160 .605 .66 60 4650 14120 90 96 422 428 0 866 597 269 .821 877 281 1.218 .716 -.284 -.482
16 260 336 245 308 15 28 247 318 247 312 2 10 0 0 56 79 59 68 13 27 6 11 43 12 .536 1.867 5 1.402 1.221 4.381 80 538 1.948 .2 100 4900 14120 88 98 445 455 -50 542 497 45 3.011 513 16 .332 8.065 1.59 3.012
17 471 822 251 343 220 479 492 799 252 345 241 456 0 0 155 197 36 51 75 100 75 96 699 697 .459 2.177 1.892 2.149 1.985 2.903 32 220 2.592 .6 70 5130 14110 88 95 469 476 0 1326 553 773 3.512 1289 735 .285 3.052 1.812 1.61
18 458 790 108 263 350 527 457 775 108 263 349 512 0 0 207 228 19 51 100 100 100 96 877 861 .664 1.506 1.467 1.705 1.717 2.218 32 226 1.666 .72 70 1290 14370 114 121 85 92 0 1274 424 850 2.429 1250 826 .412 2.366 1.28 1.243
19 170 297 113 257 57 40 150 282 115 260 37 25 0 0 67 72 25 55 56 33 42 18 97 62 1.425 .702 .676 .978 1.061 3.528 80 560 2.052 .42 100 1540 14370 113 123 109 119 -50 479 415 65 1.132 455 40 .883 1.09 .179 .124
20 187 334 122 256 65 78 164 315 133 263 42 59 0 0 88 87 66 64 27 48 16 31 143 101 .833 1.2 1.405 1.477 1.764 3.867 80 539 3.036 .32 100 1780 14370 113 123 133 143 -50 539 413 126 1.935 508 95 .517 2.266 .953 1.18

Total number of rows: 4608

Table truncated, full table size 1018 Kbytes.




Supplementary data files not provided
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