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Sample GSM79835 Query DataSets for GSM79835
Status Public on Oct 25, 2005
Title Liver (HBV+, HK1)
Sample type RNA
 
Channel 1
Source name Liver Reference 1
Organism Homo sapiens
Characteristics Liver Reference 1
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Liver (HBV+, HK1)
Organism Homo sapiens
Characteristics Liver (HBV+, HK1)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Non-tumor tissue, Liver
Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7435.gif
Data processing LOG_RAT2N_MEDIAN is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Oct 24, 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 GPL2948
Series (1)
GSE3500 Gene expression patterns in human liver cancers

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
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
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

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
1 591 376 97 55 494 321 null null 99 56 null null null null null null null null 100 100 null null null null 1.539 .65 null null .64 null 80 401 .549 .91 null null null 60 70 104 114 0 376 55 321 .65 null null 1.539 null -.622 null
2 420 196 92 53 328 143 null null 93 54 null null null null null null null null 96 100 null null null null 2.294 .436 null null .439 null 80 326 .358 .85 null null null 60 70 120 130 0 196 53 143 .436 null null 2.294 null -1.198 null
3 305 144 85 58 220 86 null null 88 60 null null null null null null null null 100 92 null null null null 2.558 .391 null null .409 null 80 319 .326 .77 null null null 60 70 135 145 0 144 58 86 .391 null null 2.558 null -1.355 null
4 152 144 83 61 69 83 null null 122 69 null null null null null null null null 0 65 null null null null .831 1.203 null null 1.233 null 80 391 .149 .75 null null null 59 70 148 159 0 144 61 83 1.203 null null .831 null .267 null
5 780 125 80 60 700 65 null null 119 67 null null null null null null null null 92 55 null null null null 10.769 .093 null null .088 null 80 388 .118 .76 null null null 59 70 164 175 0 125 60 65 .093 null null 10.769 null -3.429 null
6 666 245 78 60 588 185 null null 79 62 null null null null null null null null 100 97 null null null null 3.178 .315 null null .321 null 80 405 .284 .87 null null null 59 70 179 190 0 245 60 185 .315 null null 3.178 null -1.668 null
7 255 189 77 60 178 129 null null 79 62 null null null null null null null null 100 98 null null null null 1.38 .725 null null .744 null 52 279 .567 .75 null null null 61 69 195 203 0 189 60 129 .725 null null 1.38 null -.465 null
8 207 457 76 60 131 397 null null 79 61 null null null null null null null null 92 100 null null null null .33 3.031 null null 3.006 null 52 320 2.198 .81 null null null 62 71 211 220 0 457 60 397 3.031 null null .33 null 1.6 null
9 7306 640 78 58 7228 582 null null 79 60 null null null null null null null null 100 98 null null null null 12.419 .081 null null .083 null 80 365 .079 .93 null null null 60 70 226 236 0 640 58 582 .081 null null 12.419 null -3.635 null
10 871 3476 74 57 797 3419 null null 76 60 null null null null null null null null 100 100 null null null null .233 4.29 null null 4.239 null 52 277 3.755 .92 null null null 61 70 240 249 0 3476 57 3419 4.29 null null .233 null 2.101 null
11 318 448 78 58 240 390 null null 79 59 null null null null null null null null 92 97 null null null null .615 1.625 null null 1.631 null 80 362 1.402 .89 null null null 61 71 255 265 0 448 58 390 1.625 null null .615 null .7 null
12 856 425 81 61 775 364 null null 84 65 null null null null null null null null 100 100 null null null null 2.129 .47 null null .466 null 52 264 .418 .91 null null null 61 70 270 279 0 425 61 364 .47 null null 2.129 null -1.09 null
13 479 166 82 62 397 104 null null 85 66 null null null null null null null null 100 100 null null null null 3.817 .262 null null .273 null 80 354 .214 .84 null null null 61 71 284 294 0 166 62 104 .262 null null 3.817 null -1.933 null
14 4719 694 80 61 4639 633 null null 81 63 null null null null null null null null 100 100 null null null null 7.329 .136 null null .144 null 80 384 .126 .9 null null null 61 71 300 310 0 694 61 633 .136 null null 7.329 null -2.874 null
15 273 225 81 60 192 165 null null 81 61 null null null null null null null null 98 100 null null null null 1.164 .859 null null .843 null 80 341 .689 .86 null null null 62 72 315 325 0 225 60 165 .859 null null 1.164 null -.219 null
16 462 105 82 58 380 47 null null 82 59 null null null null null null null null 100 94 null null null null 8.085 .124 null null .114 null 52 302 .11 .73 null null null 61 70 330 339 0 105 58 47 .124 null null 8.085 null -3.015 null
17 4181 733 84 62 4097 671 null null 85 63 null null null null null null null null 100 100 null null null null 6.106 .164 null null .158 null 80 391 .143 .92 null null null 61 72 344 355 0 733 62 671 .164 null null 6.106 null -2.61 null
18 128 109 81 64 47 45 null null 83 66 null null null null null null null null 38 31 null null null null 1.044 .957 null null 1.027 null 80 355 .814 .77 null null null 61 71 359 369 -100 109 64 45 .957 null null 1.044 null -.063 null
19 1891 3162 77 63 1814 3099 null null 80 64 null null null null null null null null 100 100 null null null null .585 1.708 null null 1.689 null 52 323 1.533 .92 null null null 62 71 374 383 0 3162 63 3099 1.708 null null .585 null .773 null
20 466 263 78 59 388 204 null null 81 61 null null null null null null null null 100 100 null null null null 1.902 .526 null null .547 null 52 326 .461 .88 null null null 61 70 390 399 0 263 59 204 .526 null null 1.902 null -.927 null

Total number of rows: 24192

Table truncated, full table size 5655 Kbytes.




Supplementary data files not provided
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