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Sample GSM184342 Query DataSets for GSM184342
Status Public on Aug 09, 2007
Title GVA 105 90d A vs OVX-34-3
Sample type genomic
 
Channel 1
Source name 0.5 ug genomic DNA OVX-34
Organism Helicobacter pylori
Characteristics 0.5 ug genomic DNA OVX-34
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name 0.5 ug genomic DNA GVA 105 90d A
Organism Helicobacter pylori
Characteristics 0.5 ug genomic DNA GVA 105 90d A
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1400, 16360; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nina,,Salama
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.48; Parameter Scan Time = 08:07:59; Parameter PMT Volts = 600; Parameter Scan Date = 2006-07-07; Parameter Pixel Size = 10; Parameter Laser on time = 87395; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.51; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Nina,,Salama
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.48; Parameter Scan Time = 08:07:59; Parameter PMT Volts = 900; Parameter Scan Date = 2006-07-07; Parameter Pixel Size = 10; Parameter Laser on time = 87822; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.61; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nina,,Salama
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69237.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 Apr 25, 2007
Last update date Aug 08, 2007
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 GPL5124
Series (1)
GSE7619 Array CGH after human challenge

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 1194 336 199 119 995 217 1015 292 237 163 816 173 0 0 649 264 153 159 98 50 92 31 1212 989 4.585 .218 .212 .251 .269 3.128 208 1286 .155 .34 160 2020 17310 87 103 54 70 0 1296 459 837 .841 1126 667 1.189 .818 -.25 -.29
2 1498 351 206 107 1292 244 1299 281 241 156 1093 174 0 0 1076 299 145 157 94 51 84 32 1536 1267 5.295 .189 .159 .185 .229 4.073 208 1295 .146 .47 170 2280 17310 86 103 79 96 0 1354 413 941 .728 1084 671 1.373 .614 -.457 -.704
3 3594 935 221 111 3373 824 3575 779 252 161 3354 668 0 0 1679 633 143 160 99 88 98 78 4197 4022 4.093 .244 .199 .216 .246 2.972 156 980 .199 .67 140 2550 17310 88 102 108 122 0 3606 428 3178 .942 3005 2577 1.061 .768 -.086 -.38
4 2018 379 220 116 1798 263 1463 301 253 165 1243 185 0 0 1676 327 138 164 97 53 92 31 2061 1428 6.837 .146 .149 .166 .177 3.234 156 1070 .095 .42 150 2800 17300 86 101 132 147 0 1462 447 1014 .564 1161 714 1.772 .574 -.826 -.801
5 3586 1173 211 114 3375 1059 3622 1121 240 164 3411 1007 0 0 866 581 125 162 100 98 100 93 4434 4418 3.187 .314 .295 .274 .295 1.887 156 1009 .301 .79 140 3060 17300 87 101 159 173 0 4524 440 4085 1.21 4324 3884 .826 1.139 .275 .187
6 1351 382 195 107 1156 275 1205 357 219 159 1010 250 0 0 658 283 106 160 100 59 99 39 1431 1260 4.204 .238 .248 .212 .256 3.494 156 1083 .195 .47 150 3330 17300 86 101 185 200 0 1473 413 1061 .918 1377 964 1.09 .955 -.124 -.067
7 6529 1534 196 103 6333 1431 6584 1502 221 155 6388 1399 0 0 1728 746 137 156 100 94 99 91 7764 7787 4.426 .226 .219 .194 .216 1.87 156 1084 .218 .85 150 3580 17300 86 101 210 225 0 5917 397 5519 .872 5793 5396 1.147 .845 -.198 -.243
8 1728 520 198 117 1530 403 1607 465 229 160 1409 348 0 0 839 379 126 152 100 72 98 53 1933 1757 3.797 .263 .247 .228 .252 3.128 156 1010 .209 .52 140 3850 17300 87 101 238 252 0 2006 451 1554 1.016 1794 1342 .984 .953 .023 -.07
9 2662 720 216 119 2446 601 2643 649 238 163 2427 530 0 0 985 450 114 156 100 83 100 71 3047 2957 4.07 .246 .218 .202 .243 2.766 156 982 .2 .63 140 4110 17300 87 101 264 278 0 2777 459 2318 .948 2503 2044 1.055 .842 -.077 -.248
10 3815 1101 245 113 3570 988 3733 1009 271 161 3488 896 0 0 1097 591 151 155 100 94 100 88 4558 4384 3.613 .277 .257 .24 .263 2.011 156 1086 .257 .75 150 4360 17290 85 100 288 303 0 4247 436 3811 1.067 3892 3456 .937 .991 .094 -.013
11 9989 3873 268 116 9721 3757 7710 2372 296 163 7442 2256 0 0 6395 4092 145 152 100 98 100 94 13478 9698 2.587 .386 .303 .286 .313 2.133 156 1013 .446 .85 140 4620 17290 86 100 315 329 0 14938 447 14491 1.491 9149 8701 .671 1.169 .576 .226
12 6609 1523 314 134 6295 1389 6473 1383 369 185 6159 1249 0 0 2562 779 347 187 100 96 100 91 7684 7408 4.532 .221 .203 .205 .205 1.659 156 1044 .209 .84 140 4880 17280 85 99 341 355 0 5874 517 5357 .851 5334 4817 1.175 .782 -.233 -.354
13 4557 2148 347 134 4210 2014 4526 1698 409 187 4179 1564 0 0 1708 1553 382 193 100 95 100 85 6224 5743 2.09 .478 .374 .377 .415 2.13 120 887 .532 .84 130 5160 17280 85 98 369 382 0 8285 517 7768 1.845 6549 6032 .542 1.444 .884 .53
14 3192 782 384 127 2808 655 2532 556 412 176 2148 429 0 0 2173 805 171 167 100 79 99 60 3463 2577 4.287 .233 .2 .227 .23 2.468 156 974 .192 .59 140 5400 17280 85 99 393 407 0 3016 490 2526 .9 2145 1655 1.111 .77 -.152 -.376
15 9265 2750 414 148 8851 2602 9333 2627 448 195 8919 2479 0 0 2310 1308 181 224 100 98 100 96 11453 11398 3.402 .294 .278 .263 .294 1.763 156 1024 .29 .87 140 5670 17280 85 99 420 434 0 10607 571 10036 1.134 10132 9562 .882 1.072 .181 .1
16 8013 3153 440 134 7573 3019 7696 3104 470 184 7256 2970 0 0 3037 1893 201 171 100 99 100 97 10592 10226 2.508 .399 .409 .338 .374 1.859 156 1120 .41 .89 150 5930 17290 85 100 445 460 0 12161 517 11644 1.538 11972 11455 .65 1.579 .621 .659
17 1880 763 167 97 1713 666 1833 640 208 149 1666 543 0 0 834 530 147 155 99 90 97 72 2379 2209 2.572 .389 .326 .324 .346 2.248 156 934 .371 .7 140 2040 17550 112 126 57 71 0 2943 374 2569 1.5 2469 2094 .667 1.257 .585 .33
18 3512 910 165 91 3347 819 3285 856 195 141 3120 765 0 0 1391 549 127 144 100 92 100 85 4166 3885 4.087 .245 .245 .219 .245 2.17 156 962 .209 .68 150 2290 17540 110 125 81 96 0 3510 351 3159 .944 3302 2951 1.06 .946 -.083 -.081
19 2298 726 160 89 2138 637 2254 627 190 136 2094 538 0 0 803 515 152 142 100 83 100 69 2775 2632 3.356 .298 .257 .232 .292 2.722 156 945 .285 .69 140 2550 17550 112 126 108 122 0 2800 343 2457 1.149 2418 2075 .87 .991 .201 -.013
20 3805 1154 172 94 3633 1060 4112 1086 206 149 3940 992 0 0 1430 732 166 159 100 85 100 81 4693 4932 3.427 .292 .252 .249 .284 2.101 156 945 .29 .8 140 2810 17540 111 125 134 148 0 4451 363 4088 1.125 4189 3826 .889 .971 .17 -.042

Total number of rows: 4032

Table truncated, full table size 948 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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