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Sample GSM90614 Query DataSets for GSM90614
Status Public on Jan 05, 2006
Title Macrophage vs. UHRR
Sample type RNA
 
Channel 1
Source name 20 ug total UHRR RNA labeled with amino allyl
Organism Homo sapiens
Characteristics 20 ug total UHRR RNA labeled with amino allyl
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 20 ug total macrophage cell line RNA labeled with amino allyl
Organism Homo sapiens
Characteristics 20 ug total macrophage cell line RNA labeled with amino allyl
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Reference verification, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24755.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Jan 04, 2006
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL3305
Series (2)
GSE3972 Contribution of unique genes by individual cell lines to Universal Human Reference RNA
GSE4389 Universal Reference RNA as a standard for microarray experiments

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 LOG_RAT2N_MEDIANs 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 LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized LOG_RAT2N_MEDIAN 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 LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized LOG_RAT2N_MEDIAN 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 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
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

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
1 642 752 76 42 566 710 572 716 78 44 496 674 0 0 325 366 20 12 100 100 100 100 1276 1170 .797 1.254 1.359 1.308 1.358 1.854 52 348 1.234 .88 90 1580 9070 78 87 73 82 0 671 38 634 1.12 639 602 .893 1.213 .164 .279
2 518 547 73 43 445 504 468 554 75 45 395 511 0 0 238 180 19 14 100 100 100 100 949 906 .883 1.133 1.294 1.189 1.157 1.801 52 256 1.043 .86 80 1720 9070 79 87 88 96 0 488 38 450 1.011 495 456 .989 1.155 .016 .208
3 926 1268 79 45 847 1223 954 1342 89 59 875 1297 0 0 224 390 42 49 100 100 100 98 2070 2172 .693 1.444 1.482 1.365 1.505 1.671 80 392 1.487 .94 100 1880 9070 78 88 103 113 0 1132 40 1092 1.289 1198 1158 .776 1.323 .366 .404
4 1021 1017 84 49 937 968 1093 1074 99 71 1009 1025 0 0 456 530 49 61 100 96 100 94 1905 2034 .968 1.033 1.016 .922 .945 1.878 52 246 1.065 .93 80 2020 9070 79 87 118 126 0 908 44 864 .922 959 915 1.084 .907 -.117 -.141
5 564 592 78 45 486 547 502 541 81 47 424 496 0 0 323 352 19 16 100 100 100 100 1033 920 .888 1.126 1.17 1.07 1.118 1.737 32 212 1.047 .87 70 2160 9070 79 86 132 139 0 529 40 488 1.005 483 443 .995 1.044 .007 .063
6 1001 957 78 47 923 910 966 909 80 47 888 862 0 0 569 519 21 14 100 100 100 100 1833 1750 1.014 .986 .971 1.046 1.037 2.08 32 224 .952 .89 70 2310 9070 79 86 147 154 0 854 42 813 .88 812 770 1.136 .867 -.184 -.206
7 738 737 80 45 658 692 642 578 82 50 562 533 0 0 469 508 27 61 100 94 100 92 1350 1095 .951 1.052 .948 .997 1.13 1.879 52 258 1.079 .89 80 2450 9070 79 87 161 169 0 658 40 618 .939 516 476 1.065 .847 -.091 -.24
8 6461 11959 81 46 6380 11913 6751 12063 92 67 6670 12017 0 0 2050 3544 84 149 100 100 100 100 18293 18687 .536 1.867 1.802 1.957 1.915 1.642 52 333 1.923 .93 90 2590 9070 78 87 174 183 0 10678 41 10637 1.667 10771 10729 .6 1.609 .737 .686
9 651 651 84 47 567 604 620 557 96 64 536 510 0 0 368 347 83 119 94 96 90 86 1171 1046 .939 1.065 .951 1.144 1.071 1.91 52 257 1.022 .92 80 2740 9070 79 87 190 198 0 581 42 539 .951 497 455 1.051 .85 -.072 -.235
10 390 484 81 46 309 438 347 404 85 49 266 358 0 0 236 299 24 20 90 100 86 96 747 624 .705 1.417 1.346 1.798 1.563 2.499 52 264 1.382 .9 80 2890 9080 80 88 205 213 0 432 41 391 1.266 361 320 .79 1.202 .34 .265
11 1475 1317 83 47 1392 1270 1523 1350 86 50 1440 1303 0 0 509 516 24 17 100 100 100 100 2662 2743 1.096 .912 .905 .885 .927 1.425 80 361 .926 .96 100 3040 9080 79 89 219 229 0 1176 42 1134 .815 1205 1163 1.228 .808 -.296 -.308
12 866 1254 79 47 787 1207 838 1200 82 49 759 1153 0 0 511 642 21 16 98 100 98 100 1994 1912 .652 1.534 1.519 1.768 1.484 1.992 52 286 1.478 .92 90 3170 9070 78 87 232 241 0 1120 42 1078 1.369 1071 1029 .73 1.356 .453 .44
13 778 877 78 48 700 829 759 800 80 49 681 752 0 0 352 386 21 16 100 100 100 100 1529 1433 .844 1.184 1.104 1.24 1.161 1.733 52 253 1.166 .93 80 3320 9080 80 88 248 256 0 783 43 740 1.057 714 671 .946 .986 .081 -.02
14 383 416 78 46 305 370 333 346 79 48 255 300 0 0 257 272 19 16 96 100 94 94 675 555 .824 1.213 1.176 1.218 1.247 2.246 52 242 1.143 .9 80 3470 9080 80 88 263 271 0 371 41 330 1.083 309 268 .923 1.05 .115 .071
15 2156 4511 78 48 2078 4463 2119 4379 79 50 2041 4331 0 0 1440 2972 20 17 100 100 97 100 6541 6372 .466 2.148 2.122 2.456 2.058 2.058 80 373 2.185 .95 100 3610 9080 79 89 276 286 0 4028 43 3985 1.918 3910 3867 .521 1.895 .939 .922
16 1026 1194 77 48 949 1146 936 1227 78 49 859 1179 0 0 379 386 20 16 100 100 100 100 2095 2038 .828 1.208 1.373 1.19 1.22 1.487 52 312 1.202 .94 90 3760 9080 79 88 291 300 0 1066 43 1023 1.078 1096 1053 .927 1.225 .109 .293
17 557 541 76 46 481 495 439 397 76 47 363 351 0 0 367 383 22 14 98 98 98 98 976 714 .972 1.029 .967 .971 .911 1.69 52 312 1.034 .91 90 3910 9080 79 88 306 315 0 483 41 442 .919 354 313 1.088 .863 -.122 -.212
18 385 389 77 46 308 343 339 347 78 47 262 301 0 0 182 198 24 13 98 100 98 100 651 563 .898 1.114 1.149 1.141 1.189 1.903 52 254 1.109 .88 80 4050 9080 80 88 321 329 0 347 41 306 .994 310 269 1.006 1.026 -.008 .037
19 936 964 80 49 856 915 939 980 82 51 859 931 0 0 339 380 22 17 100 100 100 100 1771 1790 .936 1.069 1.084 1.087 1.098 1.558 80 394 1.077 .94 100 4200 9080 79 89 335 345 0 861 44 817 .954 875 831 1.048 .968 -.067 -.047
20 773 800 76 50 697 750 757 829 82 54 681 779 0 0 341 276 28 24 100 100 100 100 1447 1460 .929 1.076 1.144 1.134 1.126 1.553 32 199 1.003 .89 70 4340 9070 79 86 350 357 0 714 45 670 .961 740 696 1.041 1.021 -.058 .03

Total number of rows: 43008

Table truncated, full table size 9207 Kbytes.




Supplementary data files not provided
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