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Sample GSM39946 Query DataSets for GSM39946
Status Public on Feb 21, 2005
Title Brain, frontal cortex 2272
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Brain, frontal cortex 2272
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-05/28320.gif
 
Submission date Jan 26, 2005
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) pollack1@stanford.edu
Phone 650-736-1987
Organization name Stanford University
Department Pathology
Lab Pollack Lab
Street address 269 Campus Drive, CCSR3245A
City Stanford
State/province CA
ZIP/Postal code 94305-5176
Country USA
 
Platform ID GPL1824
Series (1)
GSE2193 Normal_human_tissues

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 same as UNF_VALUE but with flagged values removed
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
UNF_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

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 UNF_VALUE
1 147 38 86 26 61 12 150 38 87 27 64 12 0 0 31 10 19 5 90 75 76 55 73 76 5.083 .197 .188 .185 .183 2.157 52 276 .12 .5 80 1420 8790 63 71 50 58 0 45 31 14 .231 45 14 4.321 .221 -2.111 -2.181 -2.111
2 145 37 84 26 61 11 143 37 85 26 59 11 0 0 30 7 18 4 88 76 80 59 72 70 5.545 .18 .186 .17 .181 2.42 52 322 .109 .51 90 1560 8790 62 71 63 72 0 44 31 13 .212 44 13 4.714 .219 -2.237 -2.189 -2.237
3 281 101 82 26 199 75 282 101 84 26 200 75 0 0 70 23 19 4 98 100 98 100 274 275 2.653 .377 .375 .382 .387 1.653 80 349 .331 .86 100 1710 8790 62 72 78 88 0 119 31 88 .443 119 88 2.255 .441 -1.173 -1.181 -1.173
4 504 722 87 25 417 697 573 806 87 25 486 781 0 0 210 373 20 4 96 100 96 100 1114 1267 .598 1.671 1.607 1.767 1.731 1.976 52 241 1.741 .94 80 1850 8790 63 71 93 101 0 849 29 820 1.966 948 919 .509 1.891 .976 .919 .976
5 188 127 89 25 99 102 191 134 90 26 102 109 0 0 39 30 21 5 96 100 96 100 201 211 .971 1.03 1.069 1.103 .901 1.984 32 175 .739 .72 60 2000 8790 64 70 109 115 0 149 29 120 1.212 158 128 .825 1.257 .278 .33 .278
6 167 66 90 27 77 39 166 66 92 27 76 39 0 0 38 14 20 4 96 100 78 100 116 115 1.974 .506 .513 .539 .497 1.932 32 226 .323 .65 70 2140 8790 63 70 122 129 0 78 32 46 .596 78 46 1.678 .604 -.747 -.728 -.747
7 222 230 91 26 131 204 223 245 94 27 132 219 0 0 49 55 27 7 94 100 94 100 335 351 .642 1.557 1.659 1.656 1.627 1.87 52 262 1.484 .87 80 2290 8790 63 71 137 145 0 271 31 240 1.832 288 258 .546 1.952 .873 .965 .873
8 1153 917 87 27 1066 890 1234 938 88 27 1147 911 0 0 335 209 25 7 100 100 100 100 1956 2058 1.198 .835 .794 .874 .823 1.442 52 264 .794 .96 80 2440 8790 63 71 152 160 0 1079 32 1047 .982 1104 1072 1.018 .934 -.026 -.098 -.026
9 247 109 86 28 161 81 238 107 89 28 152 79 0 0 32 15 19 5 100 100 100 100 242 231 1.988 .503 .52 .505 .5 1.19 12 104 .4 .78 50 2580 8780 63 68 167 172 0 128 33 95 .592 126 93 1.69 .611 -.757 -.71 -.757
10 130 53 82 26 48 27 120 54 84 27 38 28 0 0 42 10 18 5 83 100 50 91 75 66 1.778 .563 .737 .653 .489 4.046 12 104 .167 .43 50 2730 8790 64 69 182 187 0 62 31 32 .662 64 33 1.511 .867 -.596 -.206 -.596
11 301 184 81 27 220 157 294 188 83 27 213 161 0 0 69 46 18 5 100 100 100 100 377 374 1.401 .714 .756 .717 .72 1.418 80 465 .701 .88 110 2880 8780 60 71 194 205 0 216 32 185 .84 221 189 1.191 .889 -.252 -.169 -.252
12 133 51 80 27 53 24 129 42 83 27 49 15 0 0 47 28 19 5 76 69 55 61 77 64 2.208 .453 .306 .354 .369 2.149 52 268 .42 .79 80 3020 8770 61 69 210 218 0 60 32 28 .533 49 18 1.877 .36 -.908 -1.473 -.908
13 211 104 81 27 130 77 219 100 82 27 138 73 0 0 45 21 18 5 100 100 100 100 207 211 1.688 .592 .529 .618 .556 1.534 32 203 .514 .85 70 3170 8790 63 70 225 232 0 122 32 91 .697 118 86 1.435 .622 -.521 -.684 -.521
14 163 38 84 30 79 8 138 38 87 30 54 8 0 0 65 6 26 6 91 58 58 8 87 62 9.875 .101 .148 .17 .182 4.512 12 98 .075 .48 50 3330 8770 62 67 242 247 0 45 35 9 .119 45 9 8.394 .174 -3.069 -2.52 -3.069
15 618 622 84 27 534 595 628 664 84 27 544 637 0 0 260 196 17 5 98 100 98 100 1129 1181 .897 1.114 1.171 1.212 1.15 1.458 52 261 1.033 .93 80 3460 8790 63 71 254 262 0 732 32 700 1.311 781 749 .763 1.378 .391 .462 .391
16 287 262 79 28 208 234 282 269 81 29 203 241 0 0 58 58 17 5 100 100 100 100 442 444 .889 1.125 1.187 1.132 1.16 1.426 32 224 1.117 .88 70 3600 8780 62 69 268 275 0 308 33 275 1.324 316 284 .756 1.397 .404 .482 .404
17 150 45 83 27 67 18 149 44 87 28 66 17 0 0 27 8 19 6 100 93 81 68 85 83 3.722 .269 .258 .254 .287 1.75 32 232 .176 .6 70 3760 8780 62 69 284 291 0 53 32 21 .316 52 20 3.164 .303 -1.662 -1.722 -1.662
18 161 41 86 29 75 12 161 42 88 29 75 13 0 0 35 7 19 5 93 90 87 59 87 88 6.25 .16 .173 .184 .169 2.651 32 210 .111 .55 70 3900 8780 62 69 298 305 0 48 34 14 .188 49 15 5.313 .204 -2.409 -2.294 -2.409
19 219 403 87 29 132 374 218 372 89 30 131 343 0 0 54 141 20 9 100 100 96 100 506 474 .353 2.833 2.618 2.887 2.707 1.677 52 353 3.073 .86 90 4040 8780 61 70 311 320 0 474 34 440 3.333 438 404 .3 3.08 1.737 1.623 1.737
20 175 46 88 28 87 18 178 47 91 30 90 19 0 0 33 9 26 10 96 84 78 37 105 109 4.833 .207 .211 .212 .224 2.392 32 207 .13 .59 70 4190 8790 63 70 327 334 0 54 33 21 .243 55 22 4.108 .248 -2.039 -2.009 -2.039

Total number of rows: 43008

Table truncated, full table size 8556 Kbytes.




Supplementary data files not provided
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