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Sample GSM79984 Query DataSets for GSM79984
Status Public on Oct 25, 2005
Title HCC (HBV+, HK33)
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 (HBV+, HK33)
Organism Homo sapiens
Characteristics HCC (HBV+, HK33)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tumor, Liver
Image: http://smd.stanford.edu/MicroArray/gifs//7345.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
1 931 763 56 67 875 696 null null 58 73 null null null null null null null null 100 100 null null null null 1.257 .795 null null .783 null 80 500 .774 .92 null null null 66 77 79 90 0 763 67 696 .795 null null 1.257 null -.33 null
2 540 290 56 67 484 223 null null 58 74 null null null null null null null null 98 91 null null null null 2.17 .461 null null .438 null 80 344 .42 .83 null null null 67 77 97 107 0 290 67 223 .461 null null 2.17 null -1.118 null
3 431 269 55 67 376 202 null null 57 73 null null null null null null null null 100 92 null null null null 1.861 .537 null null .52 null 80 357 .528 .85 null null null 66 77 110 121 0 269 67 202 .537 null null 1.861 null -.896 null
4 139 215 53 68 86 147 null null 55 72 null null null null null null null null 100 98 null null null null .585 1.709 null null 1.618 null 120 472 1.64 .77 null null null 65 78 124 137 0 215 68 147 1.709 null null .585 null .773 null
5 1376 261 53 68 1323 193 null null 55 70 null null null null null null null null 100 98 null null null null 6.855 .146 null null .131 null 120 411 .099 .74 null null null 66 78 141 153 0 261 68 193 .146 null null 6.855 null -2.777 null
6 954 450 55 68 899 382 null null 58 72 null null null null null null null null 100 100 null null null null 2.353 .425 null null .411 null 80 360 .401 .91 null null null 67 77 156 166 0 450 68 382 .425 null null 2.353 null -1.235 null
7 232 187 56 70 176 117 null null 61 75 null null null null null null null null 100 96 null null null null 1.504 .665 null null .639 null 52 283 .551 .76 null null null 67 75 172 180 0 187 70 117 .665 null null 1.504 null -.589 null
8 152 253 56 77 96 176 null null 65 86 null null null null null null null null 88 92 null null null null .545 1.833 null null 1.893 null 52 274 1.552 .76 null null null 68 76 188 196 0 253 77 176 1.833 null null .545 null .874 null
9 7755 1460 57 78 7698 1382 null null 59 89 null null null null null null null null 100 98 null null null null 5.57 .18 null null .186 null 80 349 .179 .95 null null null 66 76 202 212 0 1460 78 1382 .18 null null 5.57 null -2.478 null
10 1019 975 56 74 963 901 null null 56 81 null null null null null null null null 96 93 null null null null 1.069 .936 null null .929 null 80 330 .868 .94 null null null 67 77 216 226 0 975 74 901 .936 null null 1.069 null -.096 null
11 369 231 56 70 313 161 null null 58 76 null null null null null null null null 96 91 null null null null 1.944 .514 null null .508 null 80 371 .473 .86 null null null 66 76 231 241 0 231 70 161 .514 null null 1.944 null -.959 null
12 1256 330 56 70 1200 260 null null 58 76 null null null null null null null null 100 100 null null null null 4.615 .217 null null .219 null 52 277 .218 .93 null null null 67 76 247 256 0 330 70 260 .217 null null 4.615 null -2.206 null
13 709 286 60 78 649 208 null null 65 93 null null null null null null null null 100 95 null null null null 3.12 .32 null null .345 null 80 354 .292 .7 null null null 66 76 261 271 0 286 78 208 .32 null null 3.12 null -1.642 null
14 8008 1618 56 73 7952 1545 null null 61 85 null null null null null null null null 100 100 null null null null 5.147 .194 null null .199 null 80 426 .196 .95 null null null 65 76 275 286 0 1618 73 1545 .194 null null 5.147 null -2.364 null
15 298 138 55 72 243 66 null null 57 76 null null null null null null null null 98 83 null null null null 3.682 .272 null null .313 null 80 354 .244 .7 null null null 67 77 291 301 0 138 72 66 .272 null null 3.682 null -1.88 null
16 538 154 58 76 480 78 null null 59 79 null null null null null null null null 100 98 null null null null 6.154 .163 null null .158 null 52 280 .148 .75 null null null 66 75 305 314 0 154 76 78 .163 null null 6.154 null -2.621 null
17 6341 1264 60 71 6281 1193 null null 60 77 null null null null null null null null 100 98 null null null null 5.265 .19 null null .191 null 80 403 .191 .95 null null null 65 76 319 330 0 1264 71 1193 .19 null null 5.265 null -2.396 null
18 100 105 60 73 40 32 null null 61 77 null null null null null null null null 50 38 null null null null 1.25 .8 null null .808 null 80 351 .682 .72 null null null 66 76 334 344 -100 105 73 32 .8 null null 1.25 null -.322 null
19 1818 3094 62 74 1756 3020 null null 63 79 null null null null null null null null 100 100 null null null null .581 1.72 null null 1.755 null 52 304 1.671 .96 null null null 66 75 349 358 0 3094 74 3020 1.72 null null .581 null .782 null
20 444 316 59 70 385 246 null null 61 73 null null null null null null null null 96 93 null null null null 1.565 .639 null null .655 null 80 393 .601 .92 null null null 66 76 365 375 0 316 70 246 .639 null null 1.565 null -.646 null

Total number of rows: 24192

Table truncated, full table size 5635 Kbytes.




Supplementary data files not provided
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