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Sample GSM78471 Query DataSets for GSM78471
Status Public on Oct 18, 2005
Title Brain, Cerebellum
Sample type RNA
 
Channel 1
Source name CRF
Organism Homo sapiens
Characteristics CRF
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Brain, Cerebellum
Organism Homo sapiens
Characteristics Brain, Cerebellum
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Solid tumor, Brain
Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/9996.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Oct 17, 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 GPL2935
Series (2)
GSE3461 Gene expression in miscellaneous human tissues and cell lines
GSE4345 In Vivo Regulation of Human Skeletal Muscle Gene Expression by Thyroid Hormone

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 1315 1282 103 170 1212 1112 null null 110 178 null null null null null null null null 100 92 null null null null 1.09 .917 null null .691 null 52 257 .896 .81 null null null 36 44 62 70 0 2249 298 1951 1.61 null null .621 null .687 null
2 1318 1493 100 166 1218 1327 null null 146 203 null null null null null null null null 47 46 null null null null .918 1.089 null null 1.05 null 80 467 1.028 .94 null null null 33 44 74 85 0 2619 291 2328 1.911 null null .523 null .935 null
3 963 1622 108 178 855 1444 null null 174 230 null null null null null null null null 98 100 null null null null .592 1.689 null null 1.662 null 52 288 1.558 .93 null null null 37 45 94 102 0 2845 312 2533 2.963 null null .338 null 1.567 null
4 569 2542 104 203 465 2339 null null 110 207 null null null null null null null null 100 100 null null null null .199 5.03 null null 4.909 null 52 295 4.563 .93 null null null 36 44 109 117 0 4459 356 4103 8.824 null null .113 null 3.141 null
5 1942 838 120 204 1822 634 null null 144 213 null null null null null null null null 100 93 null null null null 2.874 .348 null null .323 null 32 224 .394 .89 null null null 36 43 125 132 0 1470 357 1113 .611 null null 1.637 null -.711 null
6 1277 1208 110 187 1167 1021 null null 128 196 null null null null null null null null 100 98 null null null null 1.143 .875 null null .775 null 52 345 .86 .91 null null null 35 44 138 147 0 2119 328 1791 1.535 null null .652 null .618 null
7 852 413 98 144 754 269 null null 103 152 null null null null null null null null 100 80 null null null null 2.803 .357 null null .291 null 52 285 .398 .8 null null null 36 44 155 163 0 724 252 472 .626 null null 1.597 null -.676 null
8 832 486 99 128 733 358 null null 104 133 null null null null null null null null 100 98 null null null null 2.047 .488 null null .466 null 52 257 .488 .87 null null null 35 43 169 177 0 852 224 628 .857 null null 1.167 null -.223 null
9 10618 1778 103 133 10515 1645 null null 129 141 null null null null null null null null 100 100 null null null null 6.392 .156 null null .155 null 52 354 .153 .94 null null null 33 42 182 191 0 3119 233 2886 .274 null null 3.643 null -1.865 null
10 1004 521 105 175 899 346 null null 130 184 null null null null null null null null 100 84 null null null null 2.598 .385 null null .314 null 32 180 .407 .83 null null null 35 42 200 207 0 914 307 607 .675 null null 1.481 null -.567 null
11 353 252 113 174 240 78 null null 147 186 null null null null null null null null 36 32 null null null null 3.077 .325 null null .873 null 80 525 .258 .69 null null null 33 44 208 219 0 442 305 137 .571 null null 1.752 null -.809 null
12 2463 431 109 146 2354 285 null null 155 169 null null null null null null null null 100 67 null null null null 8.26 .121 null null .115 null 52 369 .119 .53 null null null 34 43 228 237 0 756 256 500 .212 null null 4.708 null -2.235 null
13 1814 1373 104 144 1710 1229 null null 130 177 null null null null null null null null 100 98 null null null null 1.391 .719 null null .691 null 52 232 .662 .88 null null null 35 43 244 252 0 2408 252 2156 1.261 null null .793 null .334 null
14 5410 1560 109 153 5301 1407 null null 518 236 null null null null null null null null 56 56 null null null null 3.768 .265 null null .291 null 80 421 .246 .98 null null null 33 44 253 264 0 2736 268 2468 .466 null null 2.148 null -1.103 null
15 842 577 111 150 731 427 null null 515 230 null null null null null null null null 3 45 null null null null 1.712 .584 null null .595 null 80 424 .24 .86 null null null 34 44 272 282 0 1012 263 749 1.025 null null .976 null .035 null
16 2317 1073 115 176 2202 897 null null 125 185 null null null null null null null null 100 100 null null null null 2.455 .407 null null .425 null 52 262 .413 .95 null null null 35 43 287 295 0 1882 308 1574 .715 null null 1.399 null -.484 null
17 7328 2203 132 243 7196 1960 null null 140 247 null null null null null null null null 100 100 null null null null 3.671 .272 null null .273 null 52 254 .265 .97 null null null 35 43 302 310 0 3864 426 3438 .478 null null 2.093 null -1.066 null
18 398 420 132 266 266 154 null null 139 276 null null null null null null null null 70 46 null null null null 1.727 .579 null null .657 null 80 489 .571 .72 null null null 33 44 313 324 0 736 466 270 1.015 null null .985 null .022 null
19 5634 4156 134 263 5500 3893 null null 140 279 null null null null null null null null 100 100 null null null null 1.413 .708 null null .714 null 52 290 .708 .96 null null null 35 43 333 341 0 7291 461 6830 1.242 null null .805 null .312 null
20 1617 2301 131 265 1486 2036 null null 136 275 null null null null null null null null 100 100 null null null null .73 1.37 null null 1.354 null 52 267 1.258 .95 null null null 36 44 347 355 0 4036 464 3572 2.404 null null .416 null 1.265 null

Total number of rows: 24192

Table truncated, full table size 5753 Kbytes.




Supplementary data files not provided
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