NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM39908 Query DataSets for GSM39908
Status Public on Feb 21, 2005
Title Brain, occipital cortex 2273
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Brain, occipital cortex 2273
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-03/26957.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 GPL1823
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
1 156 161 93 67 63 94 160 97 92 69 67 30 0 0 36 106 23 16 84 68 71 50 157 97 .67 1.492 .448 .738 .84 4.537 32 176 3.75 .41 60 1200 7830 36 42 29 35 0 146 61 85 1.356 88 27 .737 .407 .44 -1.297 .44
2 160 161 91 69 69 92 158 143 93 73 67 74 0 0 38 70 23 20 90 90 71 75 161 141 .75 1.333 1.104 1.103 1.073 3.042 32 216 1.496 .52 70 1360 7820 34 41 44 51 0 146 63 84 1.212 130 67 .825 1.004 .278 .006 .278
3 406 204 89 66 317 138 390 187 93 69 301 121 0 0 120 68 26 21 100 100 100 94 455 422 2.297 .435 .402 .412 .375 2.056 52 271 .341 .68 80 1490 7830 35 43 57 65 0 185 60 125 .396 170 110 2.527 .365 -1.337 -1.452 -1.337
4 1136 1297 88 65 1048 1232 862 1089 91 68 774 1024 0 0 752 724 25 19 100 100 100 100 2280 1798 .851 1.176 1.323 1.297 1.139 1.648 52 334 1.1 .93 90 1640 7820 33 42 71 80 0 1179 59 1120 1.069 990 931 .936 1.203 .096 .266 .096
5 232 387 90 68 142 319 230 352 92 73 140 284 0 0 90 153 22 47 88 98 82 96 461 424 .445 2.246 2.029 2.426 2.105 1.81 52 256 2.208 .87 80 1780 7820 34 42 86 94 0 352 62 290 2.042 320 258 .49 1.844 1.03 .883 1.03
6 170 248 89 65 81 183 163 250 92 68 74 185 0 0 32 86 21 20 100 96 92 94 264 259 .443 2.259 2.5 2.058 2.245 2.213 52 277 2.769 .73 80 1930 7830 35 43 101 109 0 225 59 166 2.054 227 168 .487 2.273 1.038 1.184 1.038
7 271 404 92 67 179 337 274 394 92 69 182 327 0 0 72 127 20 19 100 100 98 100 516 509 .531 1.883 1.797 1.934 1.817 1.745 52 224 2.093 .83 80 2080 7830 35 43 116 124 0 367 61 306 1.712 358 297 .584 1.633 .775 .708 .775
8 1652 1299 90 66 1562 1233 1307 1149 92 70 1217 1083 0 0 1047 753 22 26 100 100 100 100 2795 2300 1.267 .789 .89 .842 .798 1.459 52 303 .743 .94 90 2220 7820 33 42 129 138 0 1181 60 1121 .718 1045 985 1.394 .809 -.479 -.306 -.479
9 529 323 92 62 437 261 562 325 91 63 470 263 0 0 162 84 22 17 100 100 100 100 698 733 1.674 .597 .56 .623 .539 1.845 32 218 .524 .86 70 2360 7820 34 41 144 151 0 294 56 237 .543 295 239 1.842 .509 -.881 -.975 -.881
10 219 821 92 69 127 752 217 802 96 71 125 733 0 0 72 276 33 22 90 100 78 100 879 858 .169 5.921 5.864 6.465 5.997 1.634 52 284 5.918 .85 80 2510 7820 34 42 159 167 0 746 63 684 5.383 729 666 .186 5.331 2.428 2.414 2.428
11 305 202 89 66 216 136 297 193 93 68 208 127 0 0 102 62 34 23 100 100 94 100 352 335 1.588 .63 .611 .646 .598 1.84 52 264 .572 .77 80 2660 7830 35 43 174 182 0 184 60 124 .572 175 115 1.747 .555 -.805 -.849 -.805
12 375 258 91 67 284 191 337 222 95 71 246 155 0 0 162 126 36 35 98 98 94 80 475 401 1.487 .673 .63 .634 .629 1.882 52 268 .701 .84 80 2810 7830 35 43 189 197 0 235 61 174 .611 202 141 1.636 .573 -.71 -.804 -.71
13 321 284 92 69 229 215 329 291 95 69 237 222 0 0 98 79 25 17 100 100 96 100 444 459 1.065 .939 .937 .984 .88 1.611 32 198 .836 .85 70 2940 7820 34 41 202 209 0 258 63 195 .854 265 202 1.172 .852 -.229 -.232 -.229
14 186 110 88 68 98 42 188 100 92 69 100 32 0 0 46 53 23 18 94 61 84 44 140 132 2.333 .429 .32 .357 .389 3.435 52 284 .552 .45 80 3090 7820 34 42 217 225 0 100 62 38 .39 91 29 2.567 .291 -1.36 -1.781 -1.36
15 1709 1221 88 70 1621 1151 1734 1208 91 71 1646 1138 0 0 820 321 22 26 100 100 100 100 2772 2784 1.408 .71 .691 .857 .624 2.41 52 324 .601 .87 90 3230 7820 33 42 230 239 0 1110 64 1046 .646 1098 1035 1.549 .629 -.631 -.67 -.631
16 432 449 89 68 343 381 465 456 97 87 376 388 0 0 120 103 54 175 100 100 96 65 724 764 .9 1.111 1.032 1.159 1.054 1.662 52 341 1.481 .76 90 3380 7820 33 42 245 254 0 408 62 346 1.01 415 353 .99 .938 .014 -.092 .014
17 157 99 94 68 63 31 152 81 97 70 58 13 0 0 35 54 24 18 81 34 62 15 94 71 2.032 .492 .224 .36 .357 2.864 32 172 1.055 .37 60 3530 7830 36 42 262 268 0 90 62 28 .447 74 12 2.235 .204 -1.161 -2.295 -1.161
18 175 133 89 68 86 65 180 97 92 73 91 29 0 0 40 86 24 26 96 53 81 34 151 120 1.323 .756 .319 .441 .384 4.828 32 170 2.692 .27 60 3670 7830 36 42 276 282 0 121 62 59 .687 88 26 1.455 .29 -.541 -1.787 -.541
19 240 259 87 65 153 194 222 237 89 67 135 172 0 0 73 110 19 17 100 98 96 96 347 307 .789 1.268 1.274 1.255 1.153 2.072 52 284 1.409 .79 80 3820 7830 35 43 290 298 0 235 59 176 1.153 215 156 .868 1.158 .205 .212 .205
20 181 154 88 67 93 87 183 116 91 68 95 49 0 0 45 97 21 17 96 75 87 59 180 144 1.069 .935 .516 .569 .448 3.827 32 171 2.158 .4 60 3960 7820 35 41 305 311 0 140 61 79 .85 105 45 1.176 .469 -.234 -1.093 -.234

Total number of rows: 43008

Table truncated, full table size 9197 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap