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Sample GSM79829 Query DataSets for GSM79829
Status Public on Oct 25, 2005
Title Liver (HBV+, HK36)
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+, HK36)
Organism Homo sapiens
Characteristics Liver (HBV+, HK36)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Non-tumor tissue, Liver
Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7432.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
1 753 704 81 70 672 634 null null 84 74 null null null null null null null null 98 100 null null null null 1.06 .943 null null .952 null 80 415 .788 .9 null null null 68 78 81 91 0 704 70 634 .943 null null 1.06 null -.084 null
2 579 295 76 65 503 230 null null 78 67 null null null null null null null null 97 93 null null null null 2.187 .457 null null .47 null 80 357 .414 .88 null null null 67 77 97 107 0 295 65 230 .457 null null 2.187 null -1.129 null
3 427 251 74 64 353 187 null null 77 66 null null null null null null null null 98 98 null null null null 1.888 .53 null null .549 null 80 322 .46 .85 null null null 68 78 112 122 0 251 64 187 .53 null null 1.888 null -.917 null
4 175 276 70 61 105 215 null null 72 62 null null null null null null null null 95 99 null null null null .488 2.048 null null 2.214 null 120 397 1.518 .78 null null null 67 79 126 138 0 276 61 215 2.048 null null .488 null 1.034 null
5 569 112 61 49 508 63 null null 64 54 null null null null null null null null 63 53 null null null null 8.063 .124 null null .187 null 80 346 .095 .57 null null null 67 78 141 152 0 112 49 63 .124 null null 8.063 null -3.011 null
6 366 166 49 44 317 122 null null 97 56 null null null null null null null null 43 53 null null null null 2.598 .385 null null .523 null 32 192 .275 .78 null null null 67 74 156 163 0 166 44 122 .385 null null 2.598 null -1.378 null
7 184 130 44 42 140 88 null null 97 57 null null null null null null null null 34 59 null null null null 1.591 .629 null null .636 null 32 160 .371 .57 null null null 67 73 171 177 0 130 42 88 .629 null null 1.591 null -.67 null
8 44 38 38 37 6 1 null null 48 41 null null null null null null null null 5 8 null null null null 6 .167 null null 1.286 null 80 379 .249 .48 null null null 67 77 185 195 -100 38 37 1 .167 null null 6 null -2.585 null
9 38 33 38 36 null -3 null null 46 39 null null null null null null null null 1 6 null null null null null null null null 1 null 80 337 .158 .32 null null null 66 76 200 210 -100 33 36 -3 null null null null null null null
10 37 34 37 35 null -1 null null 44 38 null null null null null null null null 2 6 null null null null null null null null 1.571 null 80 391 .232 .26 null null null 66 76 215 225 -100 34 35 -1 null null null null null null null
11 38 31 37 32 1 -1 null null 41 34 null null null null null null null null 6 8 null null null null null null null null 1.146 null 80 333 .198 .2 null null null 66 76 230 240 -100 31 32 -1 null null null null null null null
12 38 34 37 32 1 2 null null 39 34 null null null null null null null null 8 18 null null null null .5 2 null null 1.5 null 80 375 -.01 0 null null null 66 76 245 255 -100 34 32 2 2 null null .5 null 1 null
13 296 155 37 34 259 121 null null 46 39 null null null null null null null null 73 75 null null null null 2.14 .467 null null .569 null 52 295 .338 .79 null null null 69 78 262 271 0 155 34 121 .467 null null 2.14 null -1.098 null
14 7405 2279 48 41 7357 2238 null null 85 59 null null null null null null null null 100 96 null null null null 3.287 .304 null null .331 null 52 279 .281 .92 null null null 67 75 276 284 0 2279 41 2238 .304 null null 3.287 null -1.717 null
15 349 158 52 47 297 111 null null 120 83 null null null null null null null null 37 40 null null null null 2.676 .374 null null .375 null 32 191 .355 .83 null null null 65 72 291 298 0 158 47 111 .374 null null 2.676 null -1.42 null
16 39 32 40 35 -1 -3 null null 54 44 null null null null null null null null 0 0 null null null null null null null null 1.112 null 80 449 .414 .48 null null null 66 76 305 315 -100 32 35 -3 null null null null null null null
17 4465 1416 47 39 4418 1377 null null 107 56 null null null null null null null null 87 93 null null null null 3.208 .312 null null .325 null 32 175 .27 .93 null null null 67 74 325 332 0 1416 39 1377 .312 null null 3.208 null -1.682 null
18 111 148 53 48 58 100 null null 73 56 null null null null null null null null 8 27 null null null null .58 1.724 null null 1.427 null 80 346 1.51 .8 null null null 66 76 335 345 -100 148 48 100 1.724 null null .58 null .786 null
19 40 38 42 37 -2 1 null null 48 43 null null null null null null null null 2 8 null null null null null null null null 1 null 80 330 .375 .44 null null null 66 76 350 360 -100 38 37 1 null null null null null null null
20 39 37 38 34 1 3 null null 40 37 null null null null null null null null 12 15 null null null null .333 3 null null .929 null 80 330 .219 .23 null null null 66 76 365 375 -100 37 34 3 3 null null .333 null 1.585 null

Total number of rows: 24192

Table truncated, full table size 5665 Kbytes.




Supplementary data files not provided
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