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Sample GSM39909 Query DataSets for GSM39909
Status Public on Feb 21, 2005
Title Lung 0221
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Lung 0221
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-03/26250.gif
 
Submission date Jan 26, 2005
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) [email protected]
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
1 215 193 139 156 76 37 195 172 140 155 56 16 0 0 118 81 60 50 48 36 32 16 113 72 2.054 .487 .286 .649 .642 4.663 80 475 .324 .19 100 2310 7460 45 55 34 44 -50 175 142 34 .443 156 15 2.259 .26 -1.945 -1.176
2 226 253 152 160 74 93 240 234 153 166 88 74 0 0 61 87 44 48 75 62 46 40 167 162 .796 1.257 .841 .718 .776 3.661 32 164 .686 .42 60 2480 7460 47 53 53 59 0 230 145 85 1.143 213 67 .875 .764 .192 -.387 .192
3 725 1166 155 167 570 999 741 1293 156 171 586 1126 0 0 319 427 40 47 98 100 94 100 1569 1712 .571 1.753 1.922 1.956 1.844 1.547 52 333 1.67 .93 90 2610 7470 46 55 64 73 0 1060 152 908 1.593 1175 1024 .628 1.747 .672 .805 .672
4 2611 4543 160 171 2451 4372 2765 4080 160 174 2605 3909 0 0 1637 2585 43 46 98 100 96 100 6823 6514 .561 1.784 1.501 2.346 1.937 2.307 52 336 1.803 .93 90 2770 7450 44 53 80 89 0 4130 155 3975 1.622 3709 3554 .617 1.364 .697 .448 .697
5 325 488 160 173 165 315 349 465 162 175 189 292 0 0 131 127 40 36 75 98 71 98 480 481 .524 1.909 1.545 2.001 1.597 2.078 52 243 1.629 .79 80 2910 7460 46 54 95 103 0 444 157 286 1.736 423 265 .576 1.405 .795 .49 .795
6 194 222 159 184 35 38 182 198 160 184 23 14 0 0 64 72 54 53 37 37 17 13 73 37 .921 1.086 .609 .953 1.179 5.04 80 418 1.233 .18 100 3040 7450 44 54 107 117 -50 202 167 35 .987 180 13 1.013 .553 -.854 -.019
7 390 807 165 190 225 617 413 868 172 197 248 678 0 0 159 204 68 69 75 100 75 100 842 926 .365 2.742 2.734 2.908 2.454 1.897 52 306 2.315 .85 90 3200 7460 45 54 123 132 0 734 173 561 2.493 789 616 .401 2.485 1.318 1.313 1.318
8 2988 3142 147 169 2841 2973 3059 3400 151 175 2912 3231 0 0 1655 1525 48 56 98 100 96 100 5814 6143 .956 1.046 1.11 1.246 1.048 1.985 52 290 .978 .97 90 3350 7450 44 53 138 147 0 2856 154 2703 .951 3091 2937 1.051 1.009 -.072 .012 -.072
9 633 1608 145 162 488 1446 630 1665 147 163 485 1503 0 0 273 553 37 40 90 100 86 100 1934 1988 .337 2.963 3.099 3.694 3.15 2.016 52 256 2.822 .94 80 3490 7460 46 54 153 161 0 1462 147 1315 2.694 1514 1366 .371 2.817 1.43 1.494 1.43
10 394 532 146 163 248 369 235 434 146 162 89 271 0 0 932 507 35 38 81 100 62 96 617 360 .672 1.488 3.045 3.53 3.164 2.288 32 218 .354 .97 70 3630 7460 46 53 167 174 0 484 148 335 1.353 395 246 .739 2.768 .436 1.469 .436
11 569 544 146 170 423 374 565 520 149 173 419 350 0 0 318 230 38 44 94 94 86 90 797 769 1.131 .884 .835 .958 .939 1.839 52 347 .803 .9 90 3780 7460 45 54 181 190 0 495 155 340 .804 473 318 1.244 .759 -.315 -.397 -.315
12 746 525 156 192 590 333 805 511 157 190 649 319 0 0 287 139 38 48 94 98 94 96 923 968 1.772 .564 .492 .568 .569 1.7 52 263 .517 .88 80 3930 7450 45 53 197 205 0 477 175 303 .513 465 290 1.949 .447 -.963 -1.162 -.963
13 490 453 155 188 335 265 505 469 157 190 350 281 0 0 174 97 38 41 90 100 87 100 600 631 1.264 .791 .803 .754 .761 1.751 32 150 .711 .8 60 4080 7450 46 52 213 219 0 412 171 241 .719 426 255 1.391 .73 -.476 -.454 -.476
14 209 214 160 207 49 7 200 201 164 209 40 -6 0 0 71 59 42 50 48 20 31 6 56 34 7 .143 null .7 .877 2.921 80 361 .664 .27 100 4210 7440 43 53 224 234 -50 195 188 6 .13 183 null 7.7 null null -2.945
15 2952 2274 152 203 2800 2071 3118 2361 156 204 2966 2158 0 0 1084 684 40 47 100 100 96 100 4871 5124 1.352 .74 .728 .831 .735 1.82 52 271 .714 .96 90 4360 7450 44 53 239 248 0 2067 185 1883 .672 2146 1962 1.487 .661 -.573 -.596 -.573
16 1139 1183 145 192 994 991 1199 1241 148 193 1054 1049 0 0 378 332 36 44 94 100 94 100 1985 2103 1.003 .997 .995 1.067 1.012 1.717 52 246 .963 .94 90 4510 7450 44 53 254 263 0 1075 175 901 .906 1128 954 1.103 .905 -.142 -.144 -.142
17 161 188 148 192 13 -4 162 175 154 194 14 -17 0 0 48 54 41 42 25 21 7 5 9 -3 null null null 1.457 1.371 2.931 80 319 .554 .09 100 4640 7430 42 52 267 277 -50 171 175 -4 null 159 null null null null null
18 180 197 149 195 31 2 178 186 155 195 29 -9 0 0 62 52 41 43 42 16 21 7 33 20 15.5 .065 null .779 .808 4.607 80 352 -1 -1 100 4790 7430 42 52 282 292 -50 179 177 2 .059 169 null 17.05 null null -4.092
19 447 434 149 186 298 248 424 447 157 192 275 261 0 0 220 134 44 49 84 93 81 87 546 536 1.202 .832 .949 .8 .818 1.549 32 135 .722 .8 60 4930 7460 47 53 298 304 0 395 169 225 .757 406 237 1.322 .863 -.402 -.213 -.402
20 183 201 149 181 34 20 165 191 150 187 16 10 0 0 99 61 39 46 36 31 18 11 54 26 1.7 .588 .625 .774 .943 5.263 80 393 .311 .14 100 5080 7430 42 52 311 321 -50 183 165 18 .535 174 9 1.87 .568 -.816 -.903

Total number of rows: 43008

Table truncated, full table size 9270 Kbytes.




Supplementary data files not provided
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