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Sample GSM84728 Query DataSets for GSM84728
Status Public on Nov 23, 2005
Title FL11 CR 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 (FL11)
Organism Homo sapiens
Characteristics Follicular lymphoma (FL11)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18875.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 60 44 56 40 4 4 58 42 58 42 2 2 0 0 14 16 15 15 23 20 3 5 8 4 1 1 1 1.028 1.087 3.478 80 432 -1 -1 100 1630 9400 63 73 50 60 -50 57 52 5 1.299 55 3 .77 1.299 .377 .377
2 60 42 57 39 3 3 60 40 58 41 3 1 0 0 16 16 15 14 20 21 5 5 6 4 1 1 .333 .93 .643 3.825 80 343 1.012 .04 100 1780 9400 63 73 65 75 -50 55 51 4 1.299 52 1 .77 .433 .377 -1.208
3 307 315 59 40 248 275 242 262 60 42 183 222 0 0 185 207 17 16 99 98 96 98 523 405 .902 1.109 1.213 1.102 1.138 2.237 156 546 1.128 .78 140 1950 9430 64 78 80 94 0 409 52 357 1.44 340 288 .694 1.575 .526 .656
4 1128 368 60 41 1068 327 1186 386 61 45 1126 345 0 0 316 114 17 16 100 100 100 97 1395 1471 3.266 .306 .306 .297 .328 2.19 80 368 .265 .78 110 2100 9400 62 73 96 107 0 478 53 425 .398 501 448 2.515 .398 -1.33 -1.329
5 237 129 58 42 179 87 235 122 60 45 177 80 0 0 87 51 15 15 96 91 95 87 266 257 2.057 .486 .452 .438 .469 2.162 80 358 .448 .74 100 2260 9400 63 73 113 123 0 168 55 113 .631 158 104 1.584 .587 -.664 -.769
6 4777 1599 55 42 4722 1557 5057 1746 58 44 5002 1704 0 0 1535 625 16 19 100 100 100 100 6279 6706 3.033 .33 .341 .306 .34 2.457 80 430 .3 .81 110 2410 9400 62 73 127 138 0 2077 55 2022 .428 2268 2213 2.335 .442 -1.224 -1.177
7 228 88 56 39 172 49 223 87 58 42 167 48 0 0 96 39 15 15 90 82 88 61 221 215 3.51 .285 .287 .255 .317 2.978 52 310 .259 .65 90 2580 9400 63 72 145 154 0 114 51 64 .37 113 62 2.703 .373 -1.434 -1.422
8 58 44 59 39 -1 5 57 42 60 41 -2 3 0 0 14 14 16 14 15 23 1 6 4 1 null null null .999 .833 3.268 80 378 -1 -1 100 2720 9400 63 73 159 169 -50 57 51 6 null 55 4 null null null null
9 103 71 58 39 45 32 102 70 59 41 44 31 0 0 30 26 16 14 82 73 68 53 77 75 1.406 .711 .705 .771 .73 3.36 80 417 .622 .44 110 2880 9400 62 73 174 185 0 92 51 42 .924 91 40 1.083 .915 -.115 -.128
10 57 43 57 39 0 4 55 40 58 41 -2 1 0 0 17 15 16 14 16 22 2 8 4 -1 null null null .714 .8 3.425 80 372 .2 .03 100 3040 9400 63 73 191 201 -50 56 51 5 null 52 1 null null null null
11 182 95 58 41 124 54 189 91 60 42 131 50 0 0 52 36 16 14 96 87 95 71 178 181 2.296 .435 .382 .428 .402 3.246 80 370 .381 .57 100 3200 9400 63 73 207 217 0 123 53 70 .566 118 65 1.768 .496 -.822 -1.012
12 61 46 60 41 1 5 60 46 61 43 0 5 0 0 18 14 17 15 16 21 6 5 6 5 .2 5 null .96 1.163 4.153 80 358 8.858 .03 100 3350 9400 63 73 222 232 -50 60 53 6 6.494 60 6 .154 null 2.699 null
13 161 87 59 40 102 47 166 84 61 42 107 44 0 0 47 29 17 15 93 86 91 72 149 151 2.17 .461 .411 .439 .49 2.346 80 372 .402 .64 100 3510 9400 63 73 238 248 0 113 52 61 .598 109 57 1.671 .534 -.741 -.905
14 65 47 57 40 8 7 60 46 59 43 3 6 0 0 26 18 17 16 27 28 11 6 15 9 1.143 .875 2 .866 .975 3.688 80 373 10.947 .04 100 3660 9400 63 73 253 263 -50 61 52 9 1.136 60 8 .88 2.597 .184 1.377
15 146 82 56 40 90 42 145 78 59 43 89 38 0 0 46 31 16 16 92 77 90 56 132 127 2.143 .467 .427 .438 .429 2.975 80 368 .406 .5 100 3830 9400 63 73 270 280 0 106 52 55 .606 101 49 1.65 .555 -.722 -.851
16 376 261 56 40 320 221 389 253 59 43 333 213 0 0 145 111 16 14 99 100 99 100 541 546 1.448 .691 .64 .696 .675 1.948 120 564 .686 .8 130 3990 9380 59 72 284 297 0 339 52 287 .897 329 277 1.115 .831 -.157 -.268
17 58 45 56 43 2 2 54 44 60 45 -2 1 0 0 18 12 18 15 20 13 3 2 4 -1 1 1 null .666 .661 4.321 80 361 -1 -1 100 4130 9390 62 72 300 310 -50 58 56 3 1.299 57 1 .77 null .377 null
18 197 107 56 42 141 65 202 107 60 44 146 65 0 0 55 39 17 15 100 88 100 81 206 211 2.169 .461 .445 .412 .477 2.341 80 378 .418 .68 100 4300 9390 62 72 317 327 0 139 55 84 .599 139 84 1.67 .578 -.74 -.79
19 65 44 58 43 7 1 62 41 60 46 4 -2 0 0 19 13 16 16 28 12 10 3 8 2 7 .143 null .7 .623 4.644 80 379 5.755 .07 100 4450 9390 62 72 332 342 -50 57 56 1 .186 53 null 5.39 null -2.43 null
20 225 114 57 41 168 73 229 112 59 44 172 71 0 0 57 39 17 17 100 95 100 87 241 243 2.301 .435 .413 .407 .406 2.095 80 375 .357 .63 100 4620 9400 63 73 349 359 0 148 53 95 .564 145 92 1.772 .536 -.825 -.899

Total number of rows: 37632

Table truncated, full table size 7837 Kbytes.




Supplementary data files not provided
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