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Sample GSM87766 Query DataSets for GSM87766
Status Public on Dec 15, 2005
Title RA LUMC-04 sht077 vs CRC syn tis
Sample type RNA
 
Channel 1
Source name CRC
Organism Homo sapiens
Characteristics CRC
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name RA mRNA
Organism Homo sapiens
Characteristics RA mRNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Diseased tissue, Rheumatoid arthritis
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11632.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 Dec 14, 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 GPL2649
Series (2)
GSE3824 Rheumatoid arthritis and rheumatoid synovium
GSE9027 Gene expression profiling of rheumatoid arthritis synovial 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 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 72 312 62 312 10 null null null 72 326 null null null null null null null null 12 15 null null null null null null null null 3.969 null 80 239 .539 .13 null null null 48 58 95 105 0 563 563 0 null null null null null null null
2 67 314 60 286 7 28 null null 66 299 null null null null null null null null 12 21 null null null null .25 4 null null 4.329 null 80 251 .842 .18 null null null 48 58 110 120 0 566 516 51 7.214 null null .139 null 2.851 null
3 90 329 62 267 28 62 null null 77 297 null null null null null null null null 11 22 null null null null .452 2.214 null null 4.926 null 80 227 -.073 -.04 null null null 47 57 125 135 0 593 482 112 3.994 null null .25 null 1.998 null
4 144 287 83 270 61 17 null null 105 308 null null null null null null null null 33 16 null null null null 3.588 .279 null null 1.679 null 80 245 -.121 -.06 null null null 47 57 140 150 0 518 487 31 .503 null null 1.99 null -.992 null
5 141 316 85 297 56 19 null null 100 330 null null null null null null null null 37 13 null null null null 2.947 .339 null null 1.348 null 80 239 -.297 -.14 null null null 47 57 155 165 0 570 536 34 .612 null null 1.634 null -.709 null
6 60 265 65 288 -5 -23 null null 81 324 null null null null null null null null 3 3 null null null null null null null null 3.786 null 80 234 .226 .09 null null null 47 57 170 180 0 478 519 -41 null null null null null null null
7 89 279 56 280 33 -1 null null 78 301 null null null null null null null null 10 15 null null null null null null null null 3.938 null 80 234 .206 .13 null null null 47 57 185 195 0 503 505 -2 null null null null null null null
8 124 374 65 288 59 86 null null 76 308 null null null null null null null null 33 27 null null null null .686 1.458 null null 1.646 null 80 236 .456 .27 null null null 47 57 200 210 0 675 519 155 2.629 null null .38 null 1.394 null
9 603 386 66 332 537 54 null null 73 328 null null null null null null null null 100 34 null null null null 9.944 .101 null null .302 null 32 79 .135 .23 null null null 49 55 212 218 0 696 599 97 .181 null null 5.514 null -2.463 null
10 140 319 60 301 80 18 null null 63 315 null null null null null null null null 56 13 null null null null 4.444 .225 null null 1.302 null 80 301 .339 .16 null null null 46 56 229 239 0 575 543 32 .406 null null 2.464 null -1.301 null
11 138 317 60 271 78 46 null null 66 279 null null null null null null null null 48 22 null null null null 1.696 .59 null null 1.615 null 80 220 .025 0 null null null 46 56 244 254 0 572 489 83 1.064 null null .94 null .089 null
12 433 307 61 293 372 14 null null 81 306 null null null null null null null null 80 25 null null null null 26.571 .038 null null .6 null 52 158 .034 .1 null null null 47 55 257 265 0 554 528 25 .068 null null 14.733 null -3.881 null
13 141 294 61 294 80 null null null 81 300 null null null null null null null null 36 16 null null null null null null null null 1.669 null 80 289 -.097 -.05 null null null 46 56 274 284 0 530 530 0 null null null null null null null
14 362 312 92 292 270 20 null null 163 293 null null null null null null null null 56 25 null null null null 13.5 .074 null null .597 null 32 88 .044 .07 null null null 49 55 288 294 0 563 527 36 .134 null null 7.485 null -2.904 null
15 158 486 76 300 82 186 null null 104 316 null null null null null null null null 13 28 null null null null .441 2.268 null null 3.773 null 80 281 .032 0 null null null 46 56 304 314 0 877 541 335 4.091 null null .244 null 2.032 null
16 423 322 78 280 345 42 null null 95 312 null null null null null null null null 75 23 null null null null 8.214 .122 null null .419 null 80 332 .086 .13 null null null 45 55 317 327 0 581 505 76 .22 null null 4.554 null -2.187 null
17 105 345 80 295 25 50 null null 94 316 null null null null null null null null 20 21 null null null null .5 2 null null 3.885 null 80 389 .16 .09 null null null 50 60 337 347 -100 622 532 90 3.607 null null .277 null 1.851 null
18 82 304 72 307 10 -3 null null 81 313 null null null null null null null null 16 16 null null null null null null null null 4 null 80 293 -.236 -.08 null null null 50 60 352 362 -100 548 554 -5 null null null null null null null
19 544 448 71 283 473 165 null null 86 316 null null null null null null null null 92 36 null null null null 2.867 .349 null null .311 null 52 227 .138 .2 null null null 48 56 364 372 0 808 510 298 .629 null null 1.589 null -.669 null
20 148 363 90 288 58 75 null null 115 315 null null null null null null null null 21 36 null null null null .773 1.293 null null 3.295 null 80 348 .352 .25 null null null 50 60 382 392 -100 655 519 135 2.332 null null .429 null 1.222 null

Total number of rows: 24192

Table truncated, full table size 5751 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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