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Sample GSM39921 Query DataSets for GSM39921
Status Public on Feb 21, 2005
Title Lung 1351
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Lung 1351
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-02/25131.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
1 248 253 110 113 138 140 248 228 110 118 138 115 0 0 61 93 21 30 98 94 96 78 278 253 .986 1.014 .833 .882 .855 2.279 52 299 1.231 .64 80 1400 7860 42 50 28 36 0 241 108 133 .966 217 110 1.035 .794 -.05 -.333 -.05
2 190 259 108 107 82 152 184 225 110 110 76 118 0 0 39 97 21 32 100 93 87 84 234 194 .539 1.854 1.553 1.6 1.409 3.196 32 212 2.88 .52 70 1540 7850 41 48 42 49 0 247 102 145 1.765 214 112 .566 1.479 .82 .564 .82
3 573 1622 109 115 464 1507 607 1704 112 117 498 1589 0 0 158 466 24 31 100 100 100 100 1971 2087 .308 3.248 3.191 3.289 3.199 1.405 52 331 3.638 .91 90 1680 7860 41 50 55 64 0 1545 110 1435 3.093 1623 1513 .323 3.039 1.629 1.604 1.629
4 2089 3355 111 121 1978 3234 2243 3337 112 123 2132 3216 0 0 1387 1857 22 28 93 100 91 100 5212 5348 .612 1.635 1.508 1.907 1.594 2.063 80 397 1.559 .94 100 1830 7860 41 51 70 80 0 3195 115 3080 1.557 3178 3063 .642 1.437 .639 .523 .639
5 278 540 111 122 167 418 287 550 115 126 176 428 0 0 81 105 22 29 96 100 88 100 585 604 .4 2.503 2.432 2.787 2.517 1.683 52 257 2.47 .86 80 1980 7860 42 50 86 94 0 514 116 398 2.384 524 408 .419 2.316 1.253 1.212 1.253
6 193 277 120 126 73 151 194 269 121 129 74 143 0 0 35 86 26 33 90 90 81 81 224 217 .483 2.068 1.932 1.607 1.783 2.835 32 165 2.473 .58 60 2120 7850 42 48 101 107 0 264 120 144 1.97 256 136 .508 1.84 .978 .88 .978
7 362 1318 116 133 246 1185 360 1267 120 136 244 1134 0 0 114 503 25 33 96 100 96 100 1431 1378 .208 4.817 4.648 5.209 5.09 1.581 52 290 5.376 .89 90 2270 7850 40 49 114 123 0 1255 127 1129 4.588 1207 1080 .218 4.426 2.198 2.146 2.198
8 2797 2835 114 130 2683 2705 2795 2796 118 136 2681 2666 0 0 1121 937 38 39 100 100 100 100 5388 5347 .992 1.008 .994 1.083 .994 1.329 52 285 .968 .97 90 2410 7850 40 49 128 137 0 2700 124 2576 .96 2663 2539 1.041 .947 -.059 -.078 -.059
9 654 2245 111 132 543 2113 649 2385 115 137 538 2253 0 0 213 772 37 35 100 100 98 100 2656 2791 .257 3.891 4.188 3.981 3.927 1.24 52 312 3.98 .96 90 2560 7850 40 49 143 152 0 2138 126 2012 3.706 2271 2146 .27 3.988 1.89 1.996 1.89
10 200 919 107 132 93 787 201 934 109 138 94 802 0 0 52 204 22 33 88 100 80 100 880 896 .118 8.462 8.532 9.628 8.376 1.718 52 300 8.622 .8 90 2700 7850 40 49 157 166 0 875 126 750 8.059 890 764 .124 8.126 3.011 3.022 3.011
11 577 579 107 137 470 442 609 618 109 141 502 481 0 0 300 265 23 36 100 100 94 94 912 983 1.063 .94 .958 .997 .899 1.6 52 316 .915 .93 90 2840 7850 40 49 171 180 0 551 130 421 .896 589 458 1.117 .913 -.159 -.132 -.159
12 675 495 111 140 564 355 681 490 113 144 570 350 0 0 248 98 25 34 100 100 98 100 919 920 1.589 .629 .614 .691 .626 1.687 52 268 .548 .9 80 2990 7850 41 49 187 195 0 471 133 338 .599 467 333 1.668 .585 -.738 -.774 -.738
13 468 436 113 147 355 289 501 439 113 150 388 292 0 0 181 109 25 34 98 100 98 98 644 680 1.228 .814 .753 .886 .887 1.593 52 254 .753 .91 80 3140 7850 41 49 202 210 0 415 140 275 .775 418 278 1.29 .717 -.367 -.48 -.367
14 223 223 107 152 116 71 222 226 107 156 115 74 0 0 48 51 21 36 93 71 93 50 187 189 1.634 .612 .643 .563 .623 2.76 32 204 .709 .46 70 3280 7850 41 48 216 223 0 212 145 68 .583 215 70 1.715 .613 -.779 -.706 -.779
15 2721 2026 108 159 2613 1867 2884 2171 110 164 2776 2012 0 0 1113 680 24 51 100 100 100 100 4480 4788 1.4 .715 .725 .751 .69 1.36 52 306 .71 .96 90 3440 7840 39 48 231 240 0 1930 151 1778 .68 2068 1916 1.47 .69 -.555 -.535 -.555
16 984 859 105 160 879 699 1050 859 106 163 945 699 0 0 250 188 23 36 100 100 100 100 1578 1644 1.258 .795 .74 .805 .772 1.298 52 250 .772 .94 90 3580 7840 39 48 245 254 0 818 152 666 .757 818 666 1.32 .704 -.401 -.505 -.401
17 137 187 103 153 34 34 129 172 106 155 26 19 0 0 45 70 27 47 50 30 31 17 68 45 1 1 .731 1.359 1.284 3.729 80 344 3.264 .29 100 3710 7830 38 48 258 268 -50 178 146 32 .952 164 18 1.05 .696 -.523 -.07
18 152 166 108 133 44 33 138 148 111 134 30 15 0 0 52 71 27 40 52 38 35 17 77 45 1.333 .75 .5 .935 1.06 3.587 80 404 1.766 .4 100 3860 7830 38 48 273 283 -50 158 127 31 .714 141 14 1.4 .476 -1.07 -.485
19 423 333 110 132 313 201 429 310 113 129 319 178 0 0 149 86 24 31 93 100 93 100 514 497 1.557 .642 .558 .706 .624 1.897 32 162 .624 .87 60 4010 7850 42 48 290 296 0 317 126 191 .612 295 170 1.635 .531 -.709 -.912 -.709
20 214 192 110 125 104 67 215 177 113 126 105 52 0 0 43 63 21 31 93 65 93 31 171 157 1.552 .644 .495 .451 .493 2.661 32 172 1.072 .49 60 4160 7840 41 47 305 311 0 183 119 64 .614 169 50 1.63 .472 -.705 -1.084 -.705

Total number of rows: 43008

Table truncated, full table size 9324 Kbytes.




Supplementary data files not provided
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