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Sample GSM79947 Query DataSets for GSM79947
Status Public on Oct 25, 2005
Title HCC (HCV+, SF3)
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 HCC (HCV+, SF3)
Organism Homo sapiens
Characteristics HCC (HCV+, SF3)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tumor, Liver
Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7551.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 1628 2209 118 78 1510 2131 null null 136 86 null null null null null null null null 98 100 null null null null .709 1.411 null null 1.429 null 80 408 1.325 .96 null null null 42 52 63 73 0 1888 66 1822 1.207 null null .829 null .271 null
2 1045 831 97 81 948 750 null null 108 92 null null null null null null null null 100 100 null null null null 1.264 .791 null null .79 null 80 334 .711 .93 null null null 42 52 78 88 0 710 69 641 .676 null null 1.479 null -.565 null
3 822 695 91 77 731 618 null null 172 117 null null null null null null null null 45 97 null null null null 1.183 .845 null null .862 null 80 344 .624 .86 null null null 42 52 93 103 0 594 65 529 .724 null null 1.382 null -.467 null
4 278 240 84 79 194 161 null null 175 117 null null null null null null null null 0 2 null null null null 1.205 .83 null null .775 null 80 357 .346 .92 null null null 42 52 108 118 0 205 67 138 .711 null null 1.406 null -.491 null
5 3483 356 82 83 3401 273 null null 94 91 null null null null null null null null 100 100 null null null null 12.458 .08 null null .081 null 80 393 .073 .93 null null null 40 51 122 133 0 304 70 234 .069 null null 14.534 null -3.861 null
6 2272 2339 74 95 2198 2244 null null 84 102 null null null null null null null null 100 100 null null null null .98 1.021 null null 1.015 null 80 422 .957 .97 null null null 41 52 136 147 0 1999 81 1918 .873 null null 1.146 null -.197 null
7 790 673 74 94 716 579 null null 83 104 null null null null null null null null 100 100 null null null null 1.237 .809 null null .827 null 52 357 .76 .95 null null null 41 50 152 161 0 575 80 495 .691 null null 1.446 null -.533 null
8 551 1285 81 105 470 1180 null null 87 117 null null null null null null null null 100 100 null null null null .398 2.511 null null 2.67 null 32 207 2.223 .91 null null null 43 50 171 178 0 1098 89 1009 2.147 null null .466 null 1.102 null
9 20712 8549 82 97 20630 8452 null null 86 102 null null null null null null null null 100 100 null null null null 2.441 .41 null null .423 null 80 415 .411 .98 null null null 40 51 182 193 0 7306 82 7224 .35 null null 2.856 null -1.514 null
10 1963 30170 78 88 1885 30082 null null 84 94 null null null null null null null null 97 100 null null null null .063 15.959 null null 16.339 null 80 354 15.265 .97 null null null 42 52 198 208 0 25786 75 25711 13.64 null null .073 null 3.77 null
11 1217 980 81 87 1136 893 null null 89 95 null null null null null null null null 100 100 null null null null 1.272 .786 null null .794 null 52 289 .791 .95 null null null 42 51 213 222 0 837 74 763 .672 null null 1.489 null -.574 null
12 3118 1805 81 85 3037 1720 null null 94 101 null null null null null null null null 100 100 null null null null 1.766 .566 null null .568 null 52 301 .536 .96 null null null 42 51 227 236 0 1542 72 1470 .484 null null 2.066 null -1.047 null
13 2047 1786 85 92 1962 1694 null null 107 128 null null null null null null null null 100 100 null null null null 1.158 .863 null null .843 null 80 320 .815 .95 null null null 41 51 242 252 0 1526 78 1448 .738 null null 1.355 null -.438 null
14 12536 5457 80 97 12456 5360 null null 98 110 null null null null null null null null 100 100 null null null null 2.324 .43 null null .435 null 120 467 .412 .97 null null null 40 52 255 267 0 4664 82 4582 .368 null null 2.718 null -1.443 null
15 808 441 80 92 728 349 null null 88 102 null null null null null null null null 100 100 null null null null 2.086 .479 null null .481 null 80 322 .462 .94 null null null 42 52 272 282 0 376 78 298 .409 null null 2.443 null -1.289 null
16 1656 509 83 99 1573 410 null null 89 104 null null null null null null null null 100 100 null null null null 3.837 .261 null null .261 null 80 333 .247 .95 null null null 41 51 286 296 0 435 84 351 .223 null null 4.481 null -2.164 null
17 10214 7477 98 109 10116 7368 null null 114 139 null null null null null null null null 100 98 null null null null 1.373 .728 null null .712 null 120 545 .713 .96 null null null 40 53 300 313 0 6390 93 6297 .622 null null 1.606 null -.684 null
18 694 1470 102 111 592 1359 null null 107 119 null null null null null null null null 100 100 null null null null .436 2.296 null null 2.475 null 12 93 1.993 .93 null null null 43 48 318 323 0 1256 94 1162 1.963 null null .509 null .973 null
19 5026 8852 77 98 4949 8754 null null 81 105 null null null null null null null null 100 100 null null null null .565 1.769 null null 1.745 null 80 392 1.711 .97 null null null 41 51 331 341 0 7565 83 7482 1.512 null null .661 null .596 null
20 1229 1327 74 99 1155 1228 null null 76 106 null null null null null null null null 100 97 null null null null .941 1.063 null null 1.066 null 80 353 1.019 .96 null null null 41 51 346 356 0 1134 84 1050 .909 null null 1.1 null -.138 null

Total number of rows: 24192

Table truncated, full table size 5705 Kbytes.




Supplementary data files not provided
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