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Sample GSM84743 Query DataSets for GSM84743
Status Public on Nov 23, 2005
Title FL15 PR LC
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 (FL15)
Organism Homo sapiens
Characteristics Follicular lymphoma (FL15)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24123.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 GPL3113
Series (2)
GSE3647 Follicular lymphoma lymph node
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
1 132 99 121 86 11 13 126 88 124 89 5 2 0 0 31 48 29 29 21 21 5 11 24 7 .846 1.182 .4 1.267 1.205 4.321 80 423 6.985 .05 100 1890 8800 71 81 68 78 -50 85 74 11 1.019 76 2 .982 .345 .027 -1.536
2 128 97 123 86 5 11 128 88 126 91 5 2 0 0 33 39 31 32 15 20 5 8 16 7 .455 2.2 .4 .703 .89 3.133 80 410 1.973 .06 100 2040 8800 71 81 83 93 -50 84 74 9 1.897 76 2 .527 .345 .923 -1.536
3 668 989 129 87 539 902 710 1044 132 92 581 957 0 0 265 338 32 35 92 97 92 96 1441 1538 .598 1.673 1.647 1.619 1.659 1.921 80 449 1.636 .93 110 2220 8810 71 82 100 111 0 853 75 778 1.443 900 825 .693 1.42 .529 .506
4 1095 611 130 86 965 525 1182 630 133 90 1052 544 0 0 412 201 29 37 92 96 92 93 1490 1596 1.838 .544 .517 .545 .529 1.366 80 400 .513 .93 110 2370 8810 71 82 115 126 0 527 74 453 .469 543 469 2.132 .446 -1.092 -1.166
5 361 252 128 84 233 168 358 244 129 90 230 160 0 0 119 85 29 38 91 91 88 87 401 390 1.387 .721 .696 .714 .768 2.359 80 340 .646 .72 100 2520 8810 72 82 131 141 0 217 72 145 .622 210 138 1.609 .6 -.686 -.738
6 6383 3026 125 88 6258 2938 6983 3328 128 92 6858 3240 0 0 2519 1066 30 33 97 97 97 97 9196 10098 2.13 .469 .472 .51 .474 1.56 80 396 .458 .96 110 2670 8810 71 82 145 156 0 2609 76 2533 .405 2869 2793 2.471 .407 -1.305 -1.296
7 363 213 122 88 241 125 348 199 125 91 226 111 0 0 156 77 34 32 93 90 91 77 366 337 1.928 .519 .491 .515 .495 2.286 80 404 .443 .75 110 2830 8810 71 82 161 172 0 184 76 108 .447 172 96 2.236 .423 -1.161 -1.24
8 131 147 118 86 13 61 127 102 120 89 9 16 0 0 39 137 28 34 21 38 8 18 74 25 .213 4.692 1.778 1.906 2.145 3.748 80 388 6.056 .39 100 2980 8800 71 81 177 187 -50 127 74 53 4.045 88 14 .247 1.533 2.016 .616
9 190 222 118 87 72 135 184 224 120 90 66 137 0 0 65 70 28 33 78 90 56 85 207 203 .533 1.875 2.076 1.871 1.829 2.835 80 403 2.381 .52 110 3140 8810 71 82 192 203 0 191 75 116 1.616 193 118 .619 1.789 .693 .84
10 115 96 121 86 -6 10 113 90 124 88 -8 4 0 0 30 36 32 26 10 26 2 7 4 -4 null null null 1.077 .871 3.292 80 374 -1 -1 100 3290 8800 71 81 208 218 -50 83 74 9 null 78 3 null null null null
11 300 217 123 88 177 129 297 218 126 90 174 130 0 0 102 74 38 29 91 91 86 86 306 304 1.372 .729 .747 .675 .715 1.901 80 409 .669 .73 110 3450 8810 71 82 223 234 0 187 76 111 .628 188 112 1.592 .644 -.671 -.635
12 194 162 120 90 74 72 131 109 125 92 11 19 0 0 430 141 38 30 28 41 15 36 146 30 1.028 .973 1.727 1.374 1.305 4.513 80 386 .075 .18 100 3600 8800 71 81 239 249 -50 140 78 62 .839 94 16 1.192 1.489 -.254 .574
13 254 202 118 89 136 113 255 193 120 91 137 104 0 0 85 69 29 29 90 88 86 80 249 241 1.204 .831 .759 .735 .759 2.598 80 444 .798 .66 110 3760 8800 70 81 254 265 0 174 77 97 .716 166 90 1.396 .654 -.481 -.612
14 818 768 114 85 704 683 781 733 115 89 667 648 0 0 263 211 29 28 98 100 98 100 1387 1315 1.031 .97 .972 .989 .958 1.496 80 436 .911 .88 110 3930 8800 70 81 271 282 0 662 73 589 .836 632 559 1.196 .838 -.258 -.256
15 240 190 115 86 125 104 237 198 117 89 122 112 0 0 92 63 29 28 88 86 81 76 229 234 1.202 .832 .918 .787 .779 2.696 80 417 .716 .64 110 4080 8800 70 81 286 297 0 164 74 90 .717 171 97 1.394 .791 -.479 -.338
16 487 854 122 86 365 768 499 850 125 92 377 764 0 0 189 319 30 36 92 97 92 97 1133 1141 .475 2.104 2.027 2.062 2.131 1.955 80 418 2.161 .87 110 4240 8800 70 81 302 313 0 736 74 662 1.814 733 659 .551 1.747 .859 .805
17 118 95 123 87 -5 8 116 89 126 92 -7 2 0 0 28 35 33 35 10 18 1 7 3 -5 null null null .97 1.1 3.856 80 378 1.705 .05 100 4380 8790 70 80 317 327 -50 82 75 7 null 77 2 null null null null
18 403 200 118 86 285 114 405 180 122 87 287 94 0 0 122 77 31 28 93 95 93 73 399 381 2.5 .4 .328 .354 .386 2.071 80 442 .377 .7 110 4540 8800 70 81 332 343 0 172 74 98 .345 155 81 2.9 .282 -1.536 -1.824
19 126 92 120 82 6 10 128 90 124 88 8 8 0 0 27 28 33 74 15 1 2 0 16 16 .6 1.667 1 1.108 1.106 4.833 80 393 .226 .12 100 4690 8790 70 80 348 358 -50 79 71 9 1.437 78 7 .696 .862 .523 -.214
20 393 218 118 85 275 133 383 212 121 93 265 127 0 0 141 76 33 84 91 70 90 27 408 392 2.068 .484 .479 .486 .439 2.281 80 340 .425 .76 100 4850 8810 72 82 364 374 0 188 73 115 .417 183 109 2.398 .413 -1.262 -1.275

Total number of rows: 37632

Table truncated, full table size 8053 Kbytes.




Supplementary data files not provided
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