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Sample GSM39901 Query DataSets for GSM39901
Status Public on Feb 21, 2005
Title Salivary gland, parotid 0396
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Salivary gland, parotid 0396
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-03/26557.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
1 253 216 103 84 150 132 270 204 103 88 167 120 0 0 83 67 18 29 90 100 84 84 282 287 1.136 .88 .719 .749 .748 1.92 32 221 .723 .62 70 1400 7890 61 68 12 19 0 204 79 125 .83 192 113 1.205 .678 -.268 -.561 -.268
2 218 161 106 86 112 75 213 152 106 91 107 66 0 0 53 43 20 32 94 80 92 51 187 173 1.493 .67 .617 .582 .635 2.367 52 316 .639 .52 90 1540 7900 61 70 25 34 0 152 81 71 .632 143 62 1.583 .582 -.663 -.781 -.663
3 839 812 107 85 732 727 900 940 108 90 793 855 0 0 313 258 19 30 100 100 100 100 1459 1648 1.007 .993 1.078 1.041 1.029 1.521 52 322 .916 .9 90 1690 7890 60 69 40 49 0 766 80 686 .937 887 807 1.067 1.017 -.094 .025 -.094
4 2540 5743 103 95 2437 5648 2880 6326 106 96 2777 6231 0 0 1116 2546 18 31 100 100 100 100 8085 9008 .431 2.318 2.244 2.396 2.396 1.49 52 324 2.363 .95 90 1830 7890 60 69 54 63 0 5418 90 5328 2.186 5968 5878 .457 2.117 1.129 1.082 1.129
5 423 485 110 88 313 397 448 496 112 93 338 408 0 0 124 115 20 34 100 100 98 100 710 746 .788 1.268 1.207 1.382 1.314 1.68 52 276 1.238 .88 80 1980 7890 61 69 70 78 0 458 83 375 1.197 468 385 .836 1.139 .259 .187 .259
6 206 178 112 100 94 78 212 157 114 101 100 57 0 0 43 81 21 33 92 71 82 36 172 157 1.205 .83 .57 .587 .572 3.567 52 268 1.821 .33 80 2130 7890 61 69 85 93 0 168 94 74 .783 148 54 1.277 .538 -.353 -.895 -.353
7 383 214 111 101 272 113 391 210 111 104 280 109 0 0 115 38 20 32 92 100 90 94 385 389 2.407 .415 .389 .44 .381 2.133 52 232 .33 .71 80 2270 7890 61 69 99 107 0 202 95 107 .392 198 103 2.552 .367 -1.351 -1.445 -1.351
8 1823 3859 105 88 1718 3771 2019 3839 107 94 1914 3751 0 0 1040 2378 19 31 100 100 100 100 5489 5665 .456 2.195 1.96 2.266 2.253 2.201 80 381 2.336 .93 100 2420 7890 60 70 113 123 0 3641 83 3558 2.071 3622 3539 .483 1.849 1.05 .887 1.05
9 672 1352 106 97 566 1255 727 1385 106 100 621 1288 0 0 172 314 19 35 100 100 98 100 1821 1909 .451 2.217 2.074 2.332 2.079 1.53 52 244 2.284 .91 80 2560 7890 61 69 128 136 0 1275 92 1184 2.092 1307 1215 .478 1.957 1.065 .968 1.065
10 259 522 100 94 159 428 268 536 101 97 168 442 0 0 55 114 18 31 98 100 94 100 587 610 .371 2.692 2.631 2.76 2.661 1.538 52 324 2.869 .88 90 2710 7890 60 69 142 151 0 492 89 404 2.539 506 417 .394 2.482 1.345 1.312 1.345
11 579 475 98 90 481 385 606 499 101 94 508 409 0 0 166 139 19 34 100 98 100 98 866 917 1.249 .8 .805 .782 .768 1.712 52 336 .804 .89 90 2860 7890 60 69 157 166 0 448 85 363 .755 471 386 1.324 .76 -.405 -.397 -.405
12 716 535 101 102 615 433 749 541 102 108 648 439 0 0 219 148 19 36 96 98 96 98 1048 1087 1.42 .704 .677 .689 .699 2.236 52 312 .673 .87 90 3010 7890 60 69 172 181 0 505 96 408 .664 510 414 1.506 .639 -.59 -.646 -.59
13 403 390 96 97 307 293 408 377 98 104 312 280 0 0 126 122 18 34 98 100 94 98 600 592 1.048 .954 .897 .964 .954 1.795 52 243 .948 .85 80 3150 7890 61 69 187 195 0 368 92 276 .9 356 264 1.111 .847 -.151 -.24 -.151
14 193 264 94 116 99 148 196 262 94 122 102 146 0 0 49 79 16 40 96 94 94 82 247 248 .669 1.495 1.431 1.546 1.507 2.055 52 220 1.858 .68 80 3290 7890 61 69 201 209 0 249 109 140 1.41 247 138 .709 1.35 .496 .433 .496
15 1868 2182 95 125 1773 2057 1915 1914 97 131 1820 1789 0 0 777 912 19 41 98 100 98 100 3830 3609 .862 1.16 .983 1.202 1.13 1.77 52 274 1.154 .94 90 3430 7890 60 69 214 223 0 2058 118 1941 1.095 1806 1688 .914 .927 .13 -.109 .13
16 785 1163 100 108 685 1055 871 1193 102 113 771 1085 0 0 263 235 20 38 98 100 96 100 1740 1856 .649 1.54 1.407 1.711 1.461 1.828 52 312 1.435 .9 90 3580 7880 59 68 229 238 0 1097 102 995 1.453 1125 1024 .688 1.328 .539 .409 .539
17 174 143 103 100 71 43 174 150 103 104 71 50 0 0 37 42 20 32 87 65 84 18 114 121 1.651 .606 .704 .445 .575 2.872 32 220 .787 .32 70 3730 7880 60 67 245 252 0 135 94 41 .571 142 47 1.75 .664 -.808 -.59 -.808
18 200 137 104 110 96 27 217 112 104 115 113 2 0 0 56 56 19 33 81 34 78 25 123 115 3.556 .281 .018 .569 .57 7.353 32 222 7.314 .08 70 3870 7880 60 67 259 266 0 129 104 25 .265 106 2 3.769 .017 -1.914 -5.904 -1.914
19 366 364 105 96 261 268 384 362 106 102 279 266 0 0 130 112 23 33 96 100 96 100 529 545 .974 1.027 .953 1.154 1.021 1.98 32 226 .968 .81 70 4010 7880 60 67 273 280 0 343 91 253 .969 342 251 1.032 .899 -.046 -.153 -.046
20 305 322 102 107 203 215 197 139 106 109 95 32 0 0 500 712 27 40 90 48 80 25 418 127 .944 1.059 .337 .423 .366 3.927 52 350 1.134 .86 90 4160 7880 59 68 287 296 -100 304 101 203 .999 131 30 1.001 .318 -1.654 -.001

Total number of rows: 43008

Table truncated, full table size 9118 Kbytes.




Supplementary data files not provided
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