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Sample GSM39929 Query DataSets for GSM39929
Status Public on Feb 21, 2005
Title Tonsil 3011
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Tonsil 3011
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-11/35026.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
1 487 446 125 177 362 269 498 439 130 180 373 262 0 0 178 167 36 46 96 90 94 84 631 635 1.346 .743 .702 .91 .794 2.457 52 330 .629 .62 90 1610 9280 71 80 56 65 0 351 139 212 .585 346 206 1.709 .553 -.773 -.854 -.773
2 368 139 147 205 221 -66 423 134 176 208 276 -71 0 0 177 63 107 50 65 0 56 0 155 205 null null null .742 1.184 8.28 32 158 12.971 .18 60 1740 9280 73 79 71 77 0 109 161 -52 null 106 null null null null null null
3 1834 1896 134 189 1700 1707 1851 2164 150 193 1717 1975 0 0 672 845 74 51 100 100 100 100 3407 3692 .996 1.004 1.15 .898 1.047 2.4 80 440 1.073 .75 110 1900 9280 70 81 84 95 0 1493 149 1344 .791 1704 1555 1.265 .906 -.339 -.143 -.339
4 4191 9841 133 185 4058 9656 3794 9424 136 190 3661 9239 0 0 2547 6461 36 54 100 93 98 91 13714 12900 .42 2.379 2.524 1.936 2.212 4.085 80 309 3.182 .71 100 2040 9280 71 81 99 109 0 7749 146 7603 1.874 7420 7275 .534 1.987 .906 .991 .906
5 469 3085 139 192 330 2893 495 3445 144 198 356 3253 0 0 171 1145 40 48 94 100 86 100 3223 3609 .114 8.767 9.138 8.834 8.119 2.417 52 216 10.884 .71 80 2180 9290 73 81 114 122 0 2429 151 2278 6.903 2713 2561 .145 7.195 2.787 2.847 2.787
6 368 324 129 177 239 147 360 329 135 181 231 152 0 0 185 159 44 50 82 62 73 55 386 383 1.626 .615 .658 .611 .631 3.116 80 361 .52 .47 100 2330 9280 71 81 128 138 0 255 139 116 .484 259 120 2.065 .518 -1.046 -.949 -1.046
7 462 28834 126 159 336 28675 490 33755 131 167 364 33596 0 0 196 12985 35 49 88 100 88 100 29011 33960 .012 85.342 92.297 49.463 67.93 1.98 80 345 110.037 .72 100 2490 9290 72 82 144 154 0 22704 125 22579 67.199 26579 26454 .015 72.675 6.07 6.183 6.07
8 5050 22034 134 161 4916 21873 5530 26672 137 177 5396 26511 0 0 2145 12011 37 73 100 100 100 100 26789 31907 .225 4.449 4.913 3.504 4.328 3.276 80 472 6.009 .78 110 2640 9280 70 81 158 169 0 17350 127 17223 3.503 21002 20875 .285 3.869 1.809 1.952 1.809
9 981 1765 143 188 838 1577 1000 2084 150 218 857 1896 0 0 428 1074 54 104 100 90 100 78 2415 2753 .531 1.882 2.212 1.498 2.099 3.802 32 143 2.667 .74 60 2780 9270 72 78 175 181 0 1390 148 1242 1.482 1641 1493 .675 1.742 .567 .801 .567
10 270 226 140 172 130 54 221 183 143 185 81 11 0 0 153 113 47 61 57 40 46 30 184 92 2.407 .415 .136 .797 .744 3.137 52 246 .51 .39 80 2920 9280 72 80 188 196 0 178 135 43 .327 144 9 3.057 .107 -1.612 -3.225 -1.612
11 1900 3723 137 158 1763 3565 1854 3856 159 189 1717 3698 0 0 1129 2410 109 136 90 86 85 85 5328 5415 .495 2.022 2.154 1.805 1.828 3.931 120 554 2.486 .76 120 3080 9280 70 82 202 214 0 2931 124 2807 1.592 3036 2912 .628 1.696 .671 .762 .671
12 1124 2952 146 168 978 2784 1168 2811 149 207 1022 2643 0 0 701 1874 41 151 90 93 90 90 3762 3665 .351 2.847 2.586 2.396 2.3 2.424 32 184 3.398 .78 70 3230 9280 72 79 219 226 0 2324 132 2192 2.241 2213 2081 .446 2.036 1.164 1.026 1.164
13 721 1081 139 159 582 922 650 968 144 171 511 809 0 0 404 626 36 100 92 88 91 85 1504 1320 .631 1.584 1.583 1.41 1.545 2.926 80 347 1.747 .81 100 3360 9280 71 81 231 241 0 851 125 726 1.247 762 637 .802 1.247 .319 .318 .319
14 350 254 140 158 210 96 312 270 143 161 172 112 0 0 173 129 34 41 82 65 80 53 306 284 2.188 .457 .651 .611 .578 3.757 52 213 .45 .48 80 3510 9280 72 80 247 255 0 200 124 76 .36 213 88 2.778 .513 -1.474 -.964 -1.474
15 4044 17878 139 145 3905 17733 2860 14997 143 152 2721 14852 0 0 3557 14624 37 48 95 98 92 97 21638 17573 .22 4.541 5.458 3.077 4.397 5.327 80 320 5.546 .74 100 3650 9280 71 81 260 270 0 14077 114 13963 3.576 11809 11694 .28 4.298 1.838 2.104 1.838
16 1724 4358 132 145 1592 4213 1805 4699 138 151 1673 4554 0 0 1077 2747 39 51 91 97 87 93 5805 6227 .378 2.646 2.722 2.638 2.654 4.871 80 362 3.162 .78 100 3800 9280 71 81 275 285 0 3431 114 3317 2.084 3700 3586 .48 2.143 1.059 1.1 1.059
17 365 147 139 139 226 8 405 141 147 151 266 2 0 0 128 69 50 62 87 28 84 3 234 268 28.25 .035 .008 .187 .254 2.641 32 158 .083 .17 60 3940 9280 73 79 291 297 0 116 109 6 .028 111 2 35.878 .006 -5.165 -7.4 -5.165
18 420 225 138 149 282 76 491 176 157 159 353 27 0 0 164 100 70 55 83 41 75 25 358 380 3.711 .27 .076 .131 .149 3.676 12 104 .132 .2 50 4080 9280 73 78 305 310 0 177 117 60 .212 139 21 4.712 .06 -2.236 -4.053 -2.236
19 1277 2052 141 151 1136 1901 1419 2106 150 156 1278 1955 0 0 551 858 62 52 95 100 93 100 3037 3233 .598 1.673 1.53 1.692 1.601 2.534 80 436 1.75 .78 100 4240 9280 71 81 319 329 0 1616 119 1497 1.318 1658 1539 .759 1.205 .398 .268 .398
20 292 160 141 152 151 8 345 150 147 169 204 -2 0 0 180 82 54 95 57 19 57 0 159 202 18.875 .053 null .464 .46 3.983 52 234 .213 .28 80 4390 9270 71 79 335 343 -50 126 120 6 .042 118 null 23.971 null null -4.583

Total number of rows: 43008

Table truncated, full table size 9426 Kbytes.




Supplementary data files not provided
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