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Sample GSM39898 Query DataSets for GSM39898
Status Public on Feb 21, 2005
Title Thymus 0035
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Thymus 0035
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-09/20433.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
1 394 293 169 113 225 180 383 290 173 116 214 177 0 0 132 104 43 38 90 96 87 87 405 391 1.25 .8 .827 .842 .815 2.565 32 164 .666 .55 60 1300 7870 48 54 51 57 0 185 72 114 .506 184 112 1.975 .523 -.982 -.934 -.982
2 284 160 175 115 109 45 295 158 175 118 120 43 0 0 84 47 42 39 84 50 68 21 154 163 2.422 .413 .358 .488 .416 2.751 32 236 .299 .39 70 1450 7860 46 53 65 72 0 101 73 28 .261 100 27 3.827 .227 -1.936 -2.141 -1.936
3 1192 530 180 129 1012 401 1172 525 181 138 992 396 0 0 434 246 42 55 100 90 98 84 1413 1388 2.524 .396 .399 .392 .38 2.526 52 321 .384 .81 90 1610 7860 45 54 80 89 0 335 82 254 .251 332 251 3.987 .253 -1.995 -1.985 -1.995
4 3514 4654 184 155 3330 4499 3567 3962 183 163 3383 3807 0 0 1851 2572 43 60 100 100 100 100 7829 7190 .74 1.351 1.125 1.414 1.408 2.187 52 313 1.465 .86 90 1740 7860 45 54 93 102 0 2946 98 2847 .855 2508 2409 1.169 .712 -.226 -.49 -.226
5 425 744 177 161 248 583 468 750 180 170 291 589 0 0 196 266 41 60 76 100 73 94 831 880 .425 2.351 2.024 2.557 2.327 3.238 52 268 2.391 .68 80 1890 7870 47 55 109 117 0 471 102 369 1.488 475 373 .672 1.281 .573 .357 .573
6 364 324 189 170 175 154 371 336 190 183 182 166 0 0 95 121 48 76 84 75 81 62 329 348 1.136 .88 .912 1.052 1 2.084 32 164 1.093 .5 60 2020 7880 49 55 123 129 0 205 108 97 .557 213 105 1.795 .577 -.844 -.793 -.844
7 566 1585 166 183 400 1402 588 1628 182 193 422 1445 0 0 218 513 77 77 86 100 82 98 1802 1867 .285 3.505 3.424 3.493 3.422 2.498 52 282 3.778 .79 80 2180 7870 47 55 138 146 0 1003 116 887 2.218 1030 915 .451 2.167 1.149 1.116 1.149
8 5228 9957 174 171 5054 9786 5355 10897 183 186 5181 10726 0 0 2847 5750 65 76 100 100 100 100 14840 15907 .516 1.936 2.07 1.924 2.058 2.683 52 301 2.24 .83 90 2320 7860 45 54 151 160 0 6302 108 6194 1.225 6897 6789 .816 1.31 .293 .39 .293
9 947 1288 176 148 771 1140 994 1370 177 155 818 1222 0 0 325 410 42 51 100 100 100 100 1911 2040 .676 1.479 1.494 1.54 1.49 1.99 52 252 1.529 .86 80 2470 7870 47 55 167 175 0 815 94 722 .936 867 773 1.069 .945 -.096 -.081 -.096
10 364 495 166 165 198 330 371 442 174 173 205 277 0 0 118 211 87 59 82 96 63 94 528 482 .6 1.667 1.351 1.493 1.439 1.932 52 254 2.125 .64 80 2620 7870 47 55 182 190 0 313 104 209 1.055 280 175 .948 .855 .077 -.226 .077
11 1086 1485 176 162 910 1323 1089 1638 183 172 913 1476 0 0 605 690 88 59 92 98 88 98 2233 2389 .688 1.454 1.617 1.572 1.509 2.728 52 274 1.396 .85 80 2760 7870 47 55 196 204 0 940 103 837 .92 1037 934 1.087 1.023 -.12 .033 -.12
12 1352 2030 186 181 1166 1849 1446 2191 190 196 1260 2010 0 0 385 628 54 88 100 98 98 96 3015 3270 .631 1.586 1.595 1.541 1.61 2.071 52 312 1.689 .86 90 2910 7870 46 55 210 219 0 1285 115 1170 1.004 1387 1272 .996 1.01 .005 .014 .005
13 896 1232 203 202 693 1030 1020 1284 205 213 817 1082 0 0 367 411 50 74 94 96 92 96 1723 1899 .673 1.486 1.324 1.586 1.491 3.015 52 254 1.434 .85 80 3050 7870 47 55 225 233 0 780 128 652 .941 813 685 1.063 .838 -.088 -.255 -.088
14 436 923 208 203 228 720 447 973 212 215 239 770 0 0 136 307 46 72 90 94 82 94 948 1009 .317 3.158 3.222 2.839 3.251 2.525 52 313 3.636 .72 90 3200 7870 46 55 239 248 0 584 128 456 1.999 616 487 .5 2.039 .999 1.028 .999
15 7427 7636 209 203 7218 7433 8561 8871 214 210 8352 8668 0 0 2655 3524 48 56 100 100 100 100 14651 17020 .971 1.03 1.038 .868 1.081 2.65 52 323 1.105 .9 90 3340 7860 45 54 253 262 0 4833 128 4704 .652 5615 5486 1.534 .657 -.618 -.606 -.618
16 2049 2215 209 195 1840 2020 2159 2475 213 201 1950 2280 0 0 550 781 44 55 96 98 96 98 3860 4230 .911 1.098 1.169 .964 1.183 2.703 52 339 1.184 .88 90 3490 7860 45 54 268 277 0 1402 123 1278 .695 1566 1443 1.439 .74 -.525 -.434 -.525
17 318 344 193 185 125 159 315 317 196 191 122 132 0 0 86 118 46 55 86 88 65 61 284 254 .786 1.272 1.082 1.314 1.411 2.282 52 272 1.984 .52 80 3650 7870 47 55 285 293 0 218 117 101 .805 201 84 1.242 .685 -.313 -.546 -.313
18 324 336 184 181 140 155 314 319 191 196 130 138 0 0 107 108 48 109 84 65 61 28 295 268 .903 1.107 1.062 1.113 1.067 2.998 52 255 2.561 .42 80 3780 7870 47 55 298 306 0 213 115 98 .701 202 87 1.427 .672 -.513 -.574 -.513
19 878 1620 172 167 706 1453 790 1363 179 176 618 1196 0 0 499 1006 43 60 94 94 94 94 2159 1814 .486 2.058 1.935 1.954 2.185 2.305 52 296 2.245 .87 80 3930 7870 47 55 313 321 0 1025 106 920 1.303 863 757 .768 1.225 .381 .293 .381
20 383 306 173 177 210 129 385 332 178 181 212 155 0 0 112 104 42 56 90 81 87 62 339 367 1.628 .614 .731 .562 .657 2.391 32 214 .711 .51 70 4080 7870 47 54 328 335 0 194 112 82 .389 210 98 2.572 .463 -1.363 -1.112 -1.363

Total number of rows: 43008

Table truncated, full table size 9572 Kbytes.




Supplementary data files not provided
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