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Sample GSM79949 Query DataSets for GSM79949
Status Public on Oct 25, 2005
Title HCC (HBV+, SF32)
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+, SF32)
Organism Homo sapiens
Characteristics HCC (HBV+, SF32)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tumor, Liver
Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7552.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 1002 595 45 46 957 549 null null 47 48 null null null null null null null null 100 100 null null null null 1.743 .574 null null .581 null 80 413 .55 .96 null null null 42 52 70 80 0 838 64 774 .809 null null 1.236 null -.306 null
2 611 232 45 44 566 188 null null 53 47 null null null null null null null null 98 98 null null null null 3.011 .332 null null .318 null 80 352 .305 .92 null null null 42 52 85 95 0 326 61 265 .468 null null 2.136 null -1.095 null
3 457 176 44 43 413 133 null null 46 46 null null null null null null null null 100 97 null null null null 3.105 .322 null null .309 null 80 390 .303 .89 null null null 41 52 100 111 0 247 60 187 .453 null null 2.209 null -1.143 null
4 150 187 46 43 104 144 null null 48 46 null null null null null null null null 97 98 null null null null .722 1.385 null null 1.324 null 80 336 1.125 .81 null null null 42 52 115 125 0 263 60 203 1.952 null null .512 null .965 null
5 2191 297 45 42 2146 255 null null 47 45 null null null null null null null null 100 98 null null null null 8.416 .119 null null .12 null 80 374 .113 .93 null null null 40 51 129 140 0 418 59 359 .167 null null 5.978 null -2.58 null
6 804 304 43 43 761 261 null null 44 45 null null null null null null null null 100 100 null null null null 2.916 .343 null null .356 null 80 393 .317 .86 null null null 41 52 143 154 0 428 60 368 .484 null null 2.068 null -1.048 null
7 217 101 42 44 175 57 null null 43 45 null null null null null null null null 98 95 null null null null 3.07 .326 null null .31 null 80 371 .294 .81 null null null 42 52 160 170 0 142 61 81 .463 null null 2.16 null -1.111 null
8 122 121 42 46 80 75 null null 44 48 null null null null null null null null 93 92 null null null null 1.067 .938 null null .933 null 80 337 .741 .79 null null null 42 52 175 185 0 170 64 106 1.325 null null .755 null .406 null
9 7391 545 42 44 7349 501 null null 44 47 null null null null null null null null 100 100 null null null null 14.669 .068 null null .067 null 80 391 .066 .96 null null null 40 51 189 200 0 767 61 706 .096 null null 10.409 null -3.38 null
10 943 933 41 46 902 887 null null 48 51 null null null null null null null null 100 100 null null null null 1.017 .983 null null .97 null 80 335 .92 .96 null null null 41 51 205 215 0 1314 64 1250 1.386 null null .722 null .471 null
11 328 185 40 46 288 139 null null 42 49 null null null null null null null null 97 93 null null null null 2.072 .483 null null .458 null 80 383 .432 .89 null null null 41 52 218 229 0 260 64 196 .681 null null 1.469 null -.555 null
12 991 587 40 45 951 542 null null 41 47 null null null null null null null null 100 98 null null null null 1.755 .57 null null .563 null 80 341 .544 .96 null null null 42 52 235 245 0 826 63 763 .802 null null 1.246 null -.318 null
13 761 358 40 46 721 312 null null 42 49 null null null null null null null null 100 100 null null null null 2.311 .433 null null .418 null 80 369 .392 .93 null null null 41 52 248 259 0 504 64 440 .61 null null 1.639 null -.712 null
14 8219 1533 40 45 8179 1488 null null 42 46 null null null null null null null null 100 100 null null null null 5.497 .182 null null .176 null 80 365 .172 .96 null null null 42 52 264 274 0 2159 63 2096 .256 null null 3.902 null -1.964 null
15 295 103 39 45 256 58 null null 41 47 null null null null null null null null 100 95 null null null null 4.414 .227 null null .212 null 80 396 .202 .79 null null null 40 51 279 290 0 145 63 82 .32 null null 3.122 null -1.642 null
16 498 109 39 47 459 62 null null 41 49 null null null null null null null null 100 96 null null null null 7.403 .135 null null .133 null 80 323 .129 .85 null null null 41 51 294 304 0 153 66 87 .19 null null 5.276 null -2.399 null
17 5640 1479 39 46 5601 1433 null null 42 48 null null null null null null null null 100 100 null null null null 3.909 .256 null null .254 null 80 360 .243 .97 null null null 41 52 307 318 0 2083 64 2019 .36 null null 2.774 null -1.472 null
18 76 67 38 46 38 21 null null 43 48 null null null null null null null null 22 35 null null null null 1.81 .553 null null 1 null 80 337 .416 .71 null null null 42 52 323 333 -100 94 64 30 .789 null null 1.267 null -.341 null
19 1684 2060 38 46 1646 2014 null null 40 51 null null null null null null null null 100 100 null null null null .817 1.224 null null 1.19 null 80 356 1.133 .97 null null null 42 52 338 348 0 2901 64 2837 1.724 null null .58 null .785 null
20 426 194 39 48 387 146 null null 40 53 null null null null null null null null 100 93 null null null null 2.651 .377 null null .364 null 80 366 .328 .83 null null null 41 51 354 364 0 273 67 206 .532 null null 1.879 null -.91 null

Total number of rows: 24192

Table truncated, full table size 5632 Kbytes.




Supplementary data files not provided
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