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Sample GSM79922 Query DataSets for GSM79922
Status Public on Oct 25, 2005
Title Liver (HBV+, HK30)
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+, HK30)
Organism Homo sapiens
Characteristics Liver (HBV+, HK30)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Non-tumor tissue, Liver
Image: http://smd.stanford.edu/MicroArray/gifs//7254.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
1 525 539 53 50 472 489 null null 54 52 null null null null null null null null 100 100 null null null null .965 1.036 null null 1.036 null 80 460 .953 .95 null null null 42 53 124 135 0 592 54 538 1.14 null null .877 null .189 null
2 392 182 53 48 339 134 null null 54 50 null null null null null null null null 96 98 null null null null 2.53 .395 null null .405 null 80 323 .349 .9 null null null 43 53 140 150 0 200 52 148 .437 null null 2.291 null -1.196 null
3 336 204 53 50 283 154 null null 54 52 null null null null null null null null 100 100 null null null null 1.838 .544 null null .543 null 80 386 .491 .91 null null null 43 54 154 165 0 224 54 170 .601 null null 1.665 null -.735 null
4 125 346 54 52 71 294 null null 56 55 null null null null null null null null 100 100 null null null null .241 4.141 null null 4.097 null 80 330 3.51 .81 null null null 44 54 170 180 0 380 57 323 4.549 null null .22 null 2.186 null
5 1327 173 54 52 1273 121 null null 55 55 null null null null null null null null 100 98 null null null null 10.521 .095 null null .094 null 80 418 .094 .89 null null null 42 53 184 195 0 190 57 133 .104 null null 9.571 null -3.259 null
6 595 257 54 50 541 207 null null 55 53 null null null null null null null null 100 98 null null null null 2.614 .383 null null .374 null 80 393 .374 .93 null null null 43 53 200 210 0 282 54 228 .421 null null 2.373 null -1.247 null
7 200 165 53 55 147 110 null null 55 58 null null null null null null null null 100 98 null null null null 1.336 .748 null null .705 null 52 271 .635 .77 null null null 44 52 215 223 0 181 60 121 .823 null null 1.215 null -.281 null
8 108 201 55 55 53 146 null null 56 57 null null null null null null null null 92 98 null null null null .363 2.755 null null 2.648 null 52 276 1.975 .76 null null null 45 53 231 239 0 220 60 160 3.019 null null .331 null 1.594 null
9 4626 722 55 59 4571 663 null null 58 79 null null null null null null null null 100 91 null null null null 6.894 .145 null null .15 null 80 398 .135 .95 null null null 44 54 246 256 0 793 64 729 .159 null null 6.27 null -2.649 null
10 787 3557 54 58 733 3499 null null 58 71 null null null null null null null null 100 100 null null null null .209 4.774 null null 4.712 null 52 293 4.488 .97 null null null 45 54 259 268 0 3908 63 3845 5.246 null null .191 null 2.391 null
11 323 384 54 54 269 330 null null 57 59 null null null null null null null null 100 100 null null null null .815 1.227 null null 1.201 null 52 346 1.123 .92 null null null 44 53 274 283 0 421 59 362 1.346 null null .743 null .428 null
12 941 1805 55 56 886 1749 null null 56 59 null null null null null null null null 100 100 null null null null .507 1.974 null null 1.894 null 52 280 1.888 .98 null null null 47 55 292 300 0 1983 61 1922 2.169 null null .461 null 1.117 null
13 450 228 58 59 392 169 null null 60 63 null null null null null null null null 100 100 null null null null 2.32 .431 null null .439 null 80 367 .401 .9 null null null 45 55 306 316 0 250 64 186 .474 null null 2.108 null -1.076 null
14 6763 1650 56 57 6707 1593 null null 58 60 null null null null null null null null 100 100 null null null null 4.21 .238 null null .241 null 80 448 .237 .98 null null null 44 55 320 331 0 1813 62 1751 .261 null null 3.83 null -1.937 null
15 273 188 57 56 216 132 null null 59 60 null null null null null null null null 100 100 null null null null 1.636 .611 null null .59 null 52 300 .518 .73 null null null 46 55 335 344 0 206 61 145 .671 null null 1.49 null -.575 null
16 469 144 55 54 414 90 null null 58 56 null null null null null null null null 100 100 null null null null 4.6 .217 null null .228 null 52 334 .203 .84 null null null 46 55 350 359 0 158 59 99 .239 null null 4.182 null -2.064 null
17 5390 1432 55 55 5335 1377 null null 57 56 null null null null null null null null 100 100 null null null null 3.874 .258 null null .252 null 80 494 .254 .97 null null null 45 56 365 376 0 1573 60 1513 .284 null null 3.526 null -1.818 null
18 205 199 54 56 151 143 null null 56 59 null null null null null null null null 100 100 null null null null 1.056 .947 null null .927 null 12 104 .829 .77 null null null 48 53 383 388 0 218 61 157 1.04 null null .962 null .056 null
19 1416 2812 55 56 1361 2756 null null 56 60 null null null null null null null null 100 100 null null null null .494 2.025 null null 2.006 null 52 318 2.011 .98 null null null 48 57 397 406 0 3090 61 3029 2.226 null null .449 null 1.154 null
20 407 219 53 57 354 162 null null 55 59 null null null null null null null null 100 100 null null null null 2.185 .458 null null .442 null 52 314 .439 .91 null null null 46 55 411 420 0 240 62 178 .503 null null 1.989 null -.992 null

Total number of rows: 24192

Table truncated, full table size 5621 Kbytes.




Supplementary data files not provided
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