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Sample GSM84706 Query DataSets for GSM84706
Status Public on Nov 23, 2005
Title FL6 CR
Sample type RNA
 
Channel 1
Source name CRG
Organism Homo sapiens
Characteristics CRG
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Follicular lymphoma (FL6)
Organism Homo sapiens
Characteristics Follicular lymphoma (FL6)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13825.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Nov 22, 2005
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 GPL3042
Series (2)
GSE3646 Follicular lymphoma and normal lymphoid tissue comparisons
GSE4351 Variation in gene expression patterns in follicular lymphoma and the response to rituximab

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
LOG_RAT2N_MEAN 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
VALUE 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 LOG_RAT2N_MEAN VALUE
1 876 1790 101 97 775 1693 860 1691 103 103 759 1594 0 0 470 852 21 38 100 100 100 100 2468 2353 .458 2.185 2.1 2.348 2.218 1.534 52 294 2.147 .95 80 1530 7330 133 141 57 65 0 2486 135 2351 3.034 2349 2214 .33 2.917 1.601 1.544
2 1120 720 100 99 1020 621 881 666 104 107 781 567 0 0 772 519 26 44 100 83 100 83 1641 1348 1.643 .609 .726 .475 .532 2.084 12 104 .609 .91 50 1670 7320 133 138 72 77 0 1000 138 863 .846 925 788 1.183 1.008 -.242 .012
3 3400 1691 107 105 3293 1586 3512 1562 111 113 3405 1457 0 0 1696 753 28 43 100 100 100 100 4879 4862 2.076 .482 .428 .496 .479 1.479 32 200 .45 .93 70 1800 7320 132 139 84 91 0 2349 146 2203 .669 2169 2024 1.495 .594 -.58 -.751
4 258 197 104 100 154 97 116 96 106 104 12 -4 0 0 475 311 24 37 35 28 22 20 251 8 1.588 .63 null 1.524 1.166 3.579 80 416 .644 .94 100 1930 7300 129 139 96 106 -50 274 139 135 .875 133 null 1.143 null -.193 null
5 1795 1071 103 99 1692 972 1737 966 103 102 1634 867 0 0 1165 726 19 34 100 96 100 96 2664 2501 1.741 .574 .531 .511 .552 1.701 32 182 .576 .95 70 2080 7320 132 139 112 119 0 1488 138 1350 .798 1342 1204 1.253 .737 -.326 -.44
6 265 192 100 101 165 91 111 105 102 107 11 4 0 0 515 283 21 49 38 28 25 15 256 15 1.813 .552 .364 1.22 1.267 3.476 80 407 .542 .94 100 2200 7300 129 139 123 133 -50 267 140 126 .766 146 6 1.305 .505 -.385 -.986
7 1939 1054 100 94 1839 960 1464 809 102 100 1364 715 0 0 1214 743 21 36 100 100 100 100 2799 2079 1.916 .522 .524 .474 .503 1.554 32 205 .529 .92 70 2350 7320 132 139 139 146 0 1464 131 1333 .725 1124 993 1.379 .728 -.464 -.458
8 1414 1142 105 99 1309 1043 1276 1074 109 110 1171 975 0 0 765 437 30 42 100 100 100 100 2352 2146 1.255 .797 .833 .881 .831 1.602 32 148 .676 .87 60 2480 7320 133 139 153 159 0 1586 138 1449 1.107 1492 1354 .904 1.156 .146 .21
9 371 279 107 103 264 176 127 139 111 113 20 36 0 0 667 379 33 45 38 45 28 30 440 56 1.5 .667 1.8 1.213 1.065 3.507 80 412 .566 .94 100 2610 7300 129 139 164 174 -50 388 143 244 .926 193 50 1.08 2.5 -.111 1.322
10 792 755 107 105 685 650 638 732 108 113 531 627 0 0 516 340 22 44 100 100 100 96 1335 1158 1.054 .949 1.181 1.079 1.007 1.526 32 157 .822 .9 60 2760 7330 134 140 181 187 0 1049 146 903 1.318 1017 871 .759 1.64 .398 .714
11 1729 2060 105 106 1624 1954 929 1400 108 116 824 1294 0 0 1789 1650 20 42 100 100 100 100 3578 2118 .831 1.203 1.57 1.477 1.474 1.768 32 170 1.041 .95 70 2890 7320 132 139 193 200 0 2861 147 2714 1.671 1944 1797 .598 2.181 .741 1.125
12 779 2016 107 113 672 1903 385 709 111 118 278 596 0 0 803 2361 31 46 67 84 59 76 2575 874 .353 2.832 2.144 2.768 3.181 2.59 52 270 2.825 .78 90 2990 7350 134 143 202 211 0 2800 157 2643 3.933 985 828 .254 2.978 1.976 1.574
13 807 995 100 96 707 899 765 961 102 100 665 865 0 0 336 359 20 37 100 100 100 100 1606 1530 .786 1.272 1.301 1.299 1.321 1.409 32 164 1.242 .94 60 3160 7320 133 139 221 227 0 1382 133 1249 1.766 1335 1201 .566 1.807 .821 .853
14 2065 862 100 100 1965 762 2030 821 102 103 1930 721 0 0 671 369 20 33 100 100 100 100 2727 2651 2.579 .388 .374 .36 .35 1.627 32 138 .391 .92 60 3300 7330 134 140 235 241 0 1197 139 1058 .539 1140 1001 1.857 .519 -.893 -.947
15 344 244 103 99 241 145 123 127 105 102 20 28 0 0 618 319 21 35 46 46 30 30 386 48 1.662 .602 1.4 1.008 .945 2.961 80 413 .519 .95 100 3420 7310 130 140 245 255 -50 339 138 201 .836 176 39 1.197 1.944 -.259 .959
16 2667 1453 104 105 2563 1348 2616 1453 106 106 2512 1348 0 0 653 445 22 37 100 100 100 100 3911 3860 1.901 .526 .537 .511 .518 1.466 32 163 .521 .91 60 3570 7320 133 139 262 268 0 2018 146 1872 .73 2018 1872 1.369 .745 -.453 -.424
17 779 707 102 104 677 603 617 535 105 106 515 431 0 0 583 528 21 35 96 100 96 93 1280 946 1.123 .891 .837 .911 .833 1.977 32 194 .916 .91 70 3700 7330 133 140 274 281 0 982 144 838 1.237 743 599 .808 1.162 .307 .217
18 909 420 108 103 801 317 897 373 111 109 789 270 0 0 550 203 24 44 98 94 92 86 1118 1059 2.527 .396 .342 .442 .401 2.784 52 274 .324 .77 80 3840 7320 132 140 288 296 0 583 143 440 .55 518 375 1.819 .475 -.863 -1.073
19 670 502 110 113 560 389 663 480 114 117 553 367 0 0 144 157 26 51 100 100 100 100 949 920 1.44 .695 .664 .669 .663 1.653 32 202 .708 .79 70 3970 7320 132 139 301 308 0 697 157 540 .965 667 510 1.037 .922 -.052 -.118
20 2027 1478 107 111 1920 1367 1528 1457 111 113 1421 1346 0 0 1281 664 21 39 100 100 100 100 3287 2767 1.405 .712 .947 .8 .771 1.755 32 206 .63 .93 70 4100 7320 132 139 314 321 0 2053 154 1899 .989 2024 1869 1.011 1.316 -.016 .396

Total number of rows: 39168

Table truncated, full table size 8530 Kbytes.




Supplementary data files not provided
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