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Sample GSM79963 Query DataSets for GSM79963
Status Public on Oct 25, 2005
Title HCC (HBV+, HK24)
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+, HK24)
Organism Homo sapiens
Characteristics HCC (HBV+, HK24)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tumor, Liver
Image: http://smd.stanford.edu/MicroArray/gifs/2000-06/6974.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
1 982 830 79 58 903 772 null null 81 62 null null null null null null null null 100 100 null null null null 1.17 .855 null null .849 null 80 395 .832 .97 null null null 51 61 91 101 0 988 69 919 1.018 null null .983 null .025 null
2 760 388 76 56 684 332 null null 78 59 null null null null null null null null 100 100 null null null null 2.06 .485 null null .486 null 52 290 .47 .95 null null null 50 59 105 114 0 461 66 395 .577 null null 1.732 null -.792 null
3 530 287 72 54 458 233 null null 74 56 null null null null null null null null 100 100 null null null null 1.966 .509 null null .507 null 80 365 .498 .93 null null null 51 61 122 132 0 341 64 277 .605 null null 1.653 null -.725 null
4 237 271 73 53 164 218 null null 76 55 null null null null null null null null 99 99 null null null null .752 1.329 null null 1.424 null 120 407 .985 .83 null null null 50 62 135 147 0 322 63 259 1.579 null null .633 null .659 null
5 1803 674 75 52 1728 622 null null 77 53 null null null null null null null null 100 100 null null null null 2.778 .36 null null .368 null 120 428 .343 .98 null null null 50 62 150 162 0 802 61 741 .429 null null 2.332 null -1.222 null
6 1163 575 76 53 1087 522 null null 77 55 null null null null null null null null 100 100 null null null null 2.082 .48 null null .481 null 80 346 .473 .97 null null null 51 61 166 176 0 684 63 621 .571 null null 1.75 null -.808 null
7 402 266 76 54 326 212 null null 79 57 null null null null null null null null 100 98 null null null null 1.538 .65 null null .674 null 52 319 .629 .95 null null null 50 59 180 189 0 316 64 252 .773 null null 1.294 null -.371 null
8 282 358 77 50 205 308 null null 80 54 null null null null null null null null 92 98 null null null null .666 1.502 null null 1.574 null 52 253 1.246 .92 null null null 53 61 197 205 0 426 59 367 1.79 null null .559 null .84 null
9 10071 2065 79 53 9992 2012 null null 81 58 null null null null null null null null 100 100 null null null null 4.966 .201 null null .203 null 80 370 .198 .98 null null null 51 61 210 220 0 2458 63 2395 .24 null null 4.172 null -2.061 null
10 1732 3575 80 55 1652 3520 null null 83 58 null null null null null null null null 100 100 null null null null .469 2.131 null null 2.126 null 52 304 2.075 .98 null null null 51 60 225 234 0 4255 65 4190 2.536 null null .394 null 1.343 null
11 652 339 80 55 572 284 null null 82 57 null null null null null null null null 100 100 null null null null 2.014 .497 null null .473 null 52 316 .468 .94 null null null 51 60 240 249 0 403 65 338 .591 null null 1.692 null -.759 null
12 1875 1009 80 57 1795 952 null null 83 59 null null null null null null null null 100 100 null null null null 1.886 .53 null null .527 null 52 312 .509 .98 null null null 52 61 255 264 0 1201 67 1134 .632 null null 1.583 null -.663 null
13 1130 409 78 55 1052 354 null null 83 59 null null null null null null null null 100 100 null null null null 2.972 .337 null null .331 null 80 373 .333 .96 null null null 51 61 271 281 0 486 65 421 .4 null null 2.499 null -1.321 null
14 13304 3328 77 54 13227 3274 null null 80 57 null null null null null null null null 100 100 null null null null 4.04 .248 null null .25 null 80 361 .242 .98 null null null 52 62 286 296 0 3961 64 3897 .295 null null 3.394 null -1.763 null
15 524 198 79 57 445 141 null null 80 60 null null null null null null null null 100 100 null null null null 3.156 .317 null null .314 null 80 327 .302 .92 null null null 52 62 300 310 0 235 67 168 .378 null null 2.649 null -1.405 null
16 866 375 78 54 788 321 null null 81 56 null null null null null null null null 100 100 null null null null 2.455 .407 null null .415 null 80 324 .386 .96 null null null 52 62 315 325 0 446 64 382 .485 null null 2.063 null -1.045 null
17 9874 5518 78 54 9796 5464 null null 81 55 null null null null null null null null 100 100 null null null null 1.793 .558 null null .558 null 80 372 .542 .98 null null null 52 62 329 339 0 6569 64 6505 .664 null null 1.506 null -.591 null
18 494 705 77 52 417 653 null null 78 54 null null null null null null null null 100 100 null null null null .639 1.566 null null 1.361 null 32 207 1.39 .87 null null null 54 61 345 352 0 839 61 778 1.866 null null .536 null .9 null
19 3504 4441 80 54 3424 4387 null null 82 57 null null null null null null null null 100 100 null null null null .78 1.281 null null 1.271 null 52 337 1.239 .98 null null null 52 61 359 368 0 5286 64 5222 1.525 null null .656 null .609 null
20 925 769 79 55 846 714 null null 82 57 null null null null null null null null 100 100 null null null null 1.185 .844 null null .851 null 52 324 .786 .96 null null null 52 61 374 383 0 915 65 850 1.005 null null .995 null .007 null

Total number of rows: 24192

Table truncated, full table size 5657 Kbytes.




Supplementary data files not provided
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