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Sample GSM78791 Query DataSets for GSM78791
Status Public on Oct 20, 2005
Title J99-C6 vs Tigr/Astra Reference
Sample type genomic
 
Channel 1
Source name 1ug Tigr genomic DNA + 1ug Astra genomic DNA
Organism Helicobacter pylori
Characteristics 1ug Tigr genomic DNA + 1ug Astra genomic DNA
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name 2 ug J99-C6 genomic DNA
Organism Helicobacter pylori
Characteristics 2 ug J99-C6 genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10856.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 5237 4715 995 650 4242 4065 null null 998 659 null null null null null null null null 92 92 null null null null 1.044 .958 null null .887 null 52 420 1 .97 null null null 66 75 57 66 0 4668 643 4025 .949 null null 1.054 null -.076 null -.076
2 2604 817 960 614 1644 203 null null 966 620 null null null null null null null null 94 65 null null null null 8.099 .123 null null .158 null 52 340 .121 .56 null null null 67 75 82 90 0 808 607 201 .122 null null 8.179 null -3.032 null -3.032
3 5940 5030 925 592 5015 4438 null null 934 597 null null null null null null null null 100 100 null null null null 1.13 .885 null null .837 null 52 340 .918 .98 null null null 67 75 106 114 0 4980 586 4394 .876 null null 1.141 null -.191 null -.191
4 2022 1194 962 608 1060 586 null null 965 623 null null null null null null null null 100 83 null null null null 1.809 .553 null null .617 null 12 104 .452 .76 null null null 67 72 132 137 0 1182 601 581 .548 null null 1.824 null -.867 null -.867
5 1127 695 922 593 205 102 null null 934 597 null null null null null null null null 36 36 null null null null 2.01 .498 null null .743 null 120 810 .236 .39 null null null 64 76 151 163 0 688 587 101 .493 null null 2.03 null -1.021 null -1.021
6 7704 2087 987 622 6717 1465 null null 1007 628 null null null null null null null null 100 98 null null null null 4.585 .218 null null .205 null 52 420 .213 .95 null null null 65 74 178 187 0 2066 615 1451 .216 null null 4.629 null -2.211 null -2.211
7 1863 1242 1071 686 792 556 null null 1069 703 null null null null null null null null 87 90 null null null null 1.424 .702 null null .713 null 32 170 .593 .81 null null null 67 73 205 211 0 1229 679 550 .694 null null 1.44 null -.526 null -.526
8 1135 736 1008 666 127 70 null null 2096 1740 null null null null null null null null 0 0 null null null null 1.814 .551 null null .625 null 120 782 1.659 .98 null null null 64 76 223 235 0 728 659 69 .543 null null 1.841 null -.88 null -.88
9 3572 2889 1009 685 2563 2204 null null 1015 687 null null null null null null null null 98 100 null null null null 1.163 .86 null null .821 null 52 332 .857 .98 null null null 66 74 250 258 0 2860 678 2182 .851 null null 1.175 null -.232 null -.232
10 1743 1257 968 651 775 606 null null 979 655 null null null null null null null null 90 96 null null null null 1.279 .782 null null .754 null 32 236 .593 .75 null null null 66 73 275 282 0 1244 644 600 .774 null null 1.292 null -.369 null -.369
11 2279 1682 1004 673 1275 1009 null null 1021 680 null null null null null null null null 93 93 null null null null 1.264 .791 null null .728 null 32 176 .83 .93 null null null 68 74 301 307 0 1665 666 999 .784 null null 1.276 null -.352 null -.352
12 5063 1129 1097 704 3966 425 null null 1101 713 null null null null null null null null 100 75 null null null null 9.332 .107 null null .118 null 52 420 .097 .81 null null null 65 74 322 331 0 1117 697 420 .106 null null 9.443 null -3.239 null -3.239
13 2842 3881 1109 767 1733 3114 null null 1131 801 null null null null null null null null 96 100 null null null null .557 1.797 null null 1.908 null 52 420 1.741 .95 null null null 65 74 345 354 0 3842 759 3083 1.779 null null .562 null .831 null .831
14 6508 4608 1148 776 5360 3832 null null 1169 798 null null null null null null null null 98 98 null null null null 1.399 .715 null null .718 null 80 650 .706 .98 null null null 65 76 368 379 0 4562 768 3794 .708 null null 1.413 null -.499 null -.499
15 2022 1004 1099 730 923 274 null null 1118 745 null null null null null null null null 87 68 null null null null 3.369 .297 null null .408 null 32 236 .291 .77 null null null 66 73 395 402 0 994 722 272 .295 null null 3.393 null -1.763 null -1.763
16 2097 1455 1072 763 1025 692 null null 1077 768 null null null null null null null null 96 88 null null null null 1.481 .675 null null .666 null 52 332 .636 .89 null null null 66 74 418 426 0 1440 755 685 .668 null null 1.496 null -.581 null -.581
17 4529 6070 1079 745 3450 5325 null null 1102 768 null null null null null null null null 100 100 null null null null .648 1.543 null null 1.494 null 52 420 1.52 .97 null null null 65 74 440 449 0 6009 737 5272 1.528 null null .654 null .612 null .612
18 2664 2264 1061 694 1603 1570 null null 1070 698 null null null null null null null null 96 96 null null null null 1.021 .979 null null .929 null 52 340 .81 .89 null null null 90 98 58 66 0 2241 687 1554 .969 null null 1.032 null -.045 null -.045
19 3225 2236 1041 676 2184 1560 null null 1057 688 null null null null null null null null 100 100 null null null null 1.4 .714 null null .731 null 52 340 .691 .93 null null null 90 98 82 90 0 2213 669 1544 .707 null null 1.415 null -.5 null -.5
20 1892 807 1124 669 768 138 null null 1138 711 null null null null null null null null 91 33 null null null null 5.565 .18 null null .238 null 12 68 .222 .68 null null null 92 96 109 113 0 799 662 137 .178 null null 5.606 null -2.487 null -2.487

Total number of rows: 4608

Table truncated, full table size 1164 Kbytes.




Supplementary data files not provided
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