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Sample GSM78763 Query DataSets for GSM78763
Status Public on Oct 20, 2005
Title 27571 vs Tigr/Astra reference
Sample type genomic
 
Channel 1
Source name 1ug Tigr genomic DNA + 1 ug Astra DNA
Organism Helicobacter pylori
Characteristics 1ug Tigr genomic DNA + 1 ug Astra DNA
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name 2 ug 27571 genomic DNA
Organism Helicobacter pylori
Characteristics 2 ug 27571 genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/6458.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 1803 1464 267 721 1536 743 null null 270 727 null null null null null null null null 96 96 null null null null 2.067 .484 null null .508 null 32 134 .46 .93 null null null 56 62 72 78 0 2870 1413 1457 .949 null null 1.054 null -.076 null -.076
2 486 650 252 697 234 null null null 254 698 null null null null null null null null 76 13 null null null null null null null null .889 null 52 320 null null null null null 53 61 96 104 0 1274 1366 null null null null null null null null null
3 710 822 267 709 443 113 null null 296 721 null null null null null null null null 91 50 null null null null 3.92 .255 null null .406 null 12 90 .304 .53 null null null 54 59 120 125 0 1611 1390 221 .499 null null 2.005 null -1.003 null -1.003
4 268 649 250 655 18 null null null 254 660 null null null null null null null null 21 22 null null null null null null null null 2.608 null 80 552 .642 .41 null null null 53 63 145 155 0 1272 1284 null null null null null null null null null
5 240 611 238 624 2 null null null 239 622 null null null null null null null null 28 25 null null null null null null null null 2.821 null 80 538 .942 .37 null null null 53 63 169 179 0 1198 1223 null null null null null null null null null
6 469 601 237 609 232 null null null 242 614 null null null null null null null null 87 28 null null null null null null null null .385 null 32 236 null null null null null 55 62 194 201 0 1178 1194 null null null null null null null null null
7 241 580 238 615 3 null null null 243 619 null null null null null null null null 12 16 null null null null null null null null 2.286 null 80 552 .304 .15 null null null 54 64 218 228 0 1137 1205 null null null null null null null null null
8 246 574 246 619 null null null null 249 616 null null null null null null null null 18 8 null null null null null null null null 2.148 null 80 552 .216 .09 null null null 54 64 242 252 0 1125 1213 null null null null null null null null null
9 560 716 250 605 310 111 null null 251 611 null null null null null null null null 93 71 null null null null 2.793 .358 null null .43 null 32 165 .387 .7 null null null 56 62 268 274 0 1403 1186 217 .7 null null 1.429 null -.515 null -.515
10 241 545 231 581 10 null null null 274 617 null null null null null null null null 0 0 null null null null null null null null 2.706 null 80 552 .514 .2 null null null 55 65 290 300 0 1068 1139 null null null null null null null null null
11 256 563 227 549 29 14 null null 247 561 null null null null null null null null 0 1 null null null null 2.071 .483 null null 2.53 null 80 552 .3 .14 null null null 55 65 314 324 0 1103 1076 27 .931 null null 1.074 null -.103 null -.103
12 768 540 222 532 546 8 null null 223 529 null null null null null null null null 90 25 null null null null 68.25 .015 null null .346 null 52 340 null null null null null 57 65 338 346 0 1058 1043 15 .027 null null 36.4 null -5.186 null -5.186
13 424 544 228 541 196 3 null null 230 543 null null null null null null null null 83 25 null null null null 65.333 .015 null null .195 null 12 104 .364 .44 null null null 58 63 366 371 0 1066 1060 6 .031 null null 32.667 null -5.03 null -5.03
14 639 808 224 503 415 305 null null 225 508 null null null null null null null null 100 93 null null null null 1.361 .735 null null .778 null 32 160 .719 .86 null null null 57 63 389 395 0 1584 986 598 1.441 null null .694 null .527 null .527
15 234 506 212 484 22 22 null null 219 486 null null null null null null null null 21 20 null null null null 1 1 null null 2.642 null 80 552 .671 .32 null null null 56 66 411 421 0 992 949 43 1.955 null null .512 null .967 null .967
16 242 499 208 481 34 18 null null 212 482 null null null null null null null null 52 37 null null null null 1.889 .529 null null 2.488 null 80 552 .603 .27 null null null 56 66 435 445 0 978 943 35 1.029 null null .971 null .042 null .042
17 266 522 207 470 59 52 null null 210 471 null null null null null null null null 66 46 null null null null 1.135 .881 null null 1 null 80 552 .345 .22 null null null 56 66 459 469 0 1023 921 102 1.729 null null .578 null .79 null .79
18 278 686 243 665 35 21 null null 247 666 null null null null null null null null 32 27 null null null null 1.667 .6 null null 2.302 null 80 552 .799 .43 null null null 77 87 73 83 0 1345 1303 42 1.2 null null .833 null .263 null .263
19 345 687 249 665 96 22 null null 254 668 null null null null null null null null 55 23 null null null null 4.364 .229 null null .961 null 80 560 .321 .33 null null null 77 87 97 107 0 1347 1303 44 .458 null null 2.182 null -1.126 null -1.126
20 266 647 255 666 11 null null null 255 668 null null null null null null null null 28 18 null null null null null null null null 1.92 null 80 560 .591 .27 null null null 77 87 121 131 0 1268 1305 null null null null null null null null null

Total number of rows: 4608

Table truncated, full table size 1126 Kbytes.




Supplementary data files not provided
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