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Sample GSM88136 Query DataSets for GSM88136
Status Public on Dec 17, 2005
Title OA LUMC-20 LC14n057 vs LCR syn tis
Sample type RNA
 
Channel 1
Source name LCR
Organism Homo sapiens
Characteristics LCR
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name OA mRNA
Organism Homo sapiens
Characteristics OA mRNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Diseased tissue, Osteoarthritis
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10573.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 16, 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 GPL3262
Series (1)
GSE3848 Arthritis and Rheumatism

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
1 170 384 131 326 39 58 null null 142 357 null null null null null null null null 21 16 null null null null .672 1.487 null null 2.688 null 80 484 .554 .23 null null null 73 83 69 79 -100 606 514 91 2.346 null null .426 null 1.23 null
2 2265 1766 131 331 2134 1435 null null 142 369 null null null null null null null null 100 96 null null null null 1.487 .672 null null .677 null 52 393 .577 .66 null null null 73 82 88 97 0 2785 522 2263 1.061 null null .943 null .085 null
3 1089 506 125 313 964 193 null null 131 359 null null null null null null null null 100 37 null null null null 4.995 .2 null null .252 null 32 170 .192 .39 null null null 76 82 110 116 0 798 494 304 .316 null null 3.167 null -1.663 null
4 2550 1020 129 324 2421 696 null null 137 359 null null null null null null null null 100 92 null null null null 3.478 .287 null null .26 null 52 374 .274 .71 null null null 74 83 124 133 0 1609 511 1098 .453 null null 2.205 null -1.141 null
5 10757 39045 128 326 10629 38719 null null 135 358 null null null null null null null null 100 100 null null null null .275 3.643 null null 3.658 null 80 461 3.51 .95 null null null 74 84 141 151 0 61585 514 61071 5.746 null null .174 null 2.522 null
6 2223 2052 132 334 2091 1718 null null 135 360 null null null null null null null null 100 100 null null null null 1.217 .822 null null .666 null 52 312 1.012 .61 null null null 75 83 159 167 0 3237 527 2710 1.296 null null .772 null .374 null
7 7828 6344 126 326 7702 6018 null null 132 352 null null null null null null null null 100 100 null null null null 1.28 .781 null null .562 null 52 321 .898 .47 null null null 76 84 176 184 0 10006 514 9492 1.232 null null .811 null .302 null
8 2252 1196 123 296 2129 900 null null 129 337 null null null null null null null null 100 96 null null null null 2.366 .423 null null .422 null 52 326 .362 .74 null null null 76 84 195 203 0 1886 467 1420 .667 null null 1.5 null -.585 null
9 6859 6324 127 320 6732 6004 null null 131 349 null null null null null null null null 100 98 null null null null 1.121 .892 null null .839 null 80 453 .877 .9 null null null 75 85 211 221 0 9975 505 9470 1.407 null null .711 null .492 null
10 2493 1496 125 334 2368 1162 null null 131 359 null null null null null null null null 100 98 null null null null 2.038 .491 null null .477 null 52 371 .423 .81 null null null 75 84 228 237 0 2360 527 1833 .774 null null 1.292 null -.37 null
11 1951 1100 119 318 1832 782 null null 131 354 null null null null null null null null 100 92 null null null null 2.343 .427 null null .461 null 52 394 .345 .73 null null null 75 84 245 254 0 1735 502 1233 .673 null null 1.485 null -.571 null
12 7388 5473 123 294 7265 5179 null null 135 325 null null null null null null null null 100 100 null null null null 1.403 .713 null null .717 null 52 397 .655 .92 null null null 75 84 263 272 0 8633 464 8169 1.124 null null .889 null .169 null
13 1569 1035 126 301 1443 734 null null 132 349 null null null null null null null null 100 90 null null null null 1.966 .509 null null .539 null 52 385 .449 .74 null null null 76 85 280 289 0 1632 475 1158 .802 null null 1.246 null -.318 null
14 482 513 132 310 350 203 null null 146 349 null null null null null null null null 100 37 null null null null 1.724 .58 null null .634 null 32 236 .202 .15 null null null 78 85 299 306 0 809 489 320 .915 null null 1.093 null -.128 null
15 325 404 124 305 201 99 null null 135 346 null null null null null null null null 85 28 null null null null 2.03 .493 null null 1.409 null 80 475 .343 .2 null null null 76 86 315 325 -100 637 481 156 .777 null null 1.287 null -.364 null
16 1192 797 125 327 1067 470 null null 131 351 null null null null null null null null 100 78 null null null null 2.27 .44 null null .471 null 52 326 .369 .57 null null null 77 85 334 342 0 1257 516 741 .695 null null 1.439 null -.525 null
17 370 466 127 332 243 134 null null 127 367 null null null null null null null null 94 30 null null null null 1.813 .551 null null .877 null 52 328 .054 .03 null null null 77 85 353 361 0 735 524 211 .87 null null 1.15 null -.201 null
18 424 545 134 360 290 185 null null 151 384 null null null null null null null null 100 46 null null null null 1.568 .638 null null .918 null 32 158 -.054 0 null null null 78 84 373 379 0 860 568 292 1.006 null null .994 null .009 null
19 316 446 133 372 183 74 null null 146 399 null null null null null null null null 75 30 null null null null 2.473 .404 null null 1.012 null 80 467 .29 .16 null null null 77 87 385 395 -100 703 587 117 .638 null null 1.568 null -.649 null
20 1230 705 129 353 1101 352 null null 137 369 null null null null null null null null 100 50 null null null null 3.128 .32 null null .282 null 52 351 .292 .47 null null null 78 87 404 413 0 1112 557 555 .504 null null 1.983 null -.988 null

Total number of rows: 18432

Table truncated, full table size 4429 Kbytes.




Supplementary data files not provided
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