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Sample GSM88125 Query DataSets for GSM88125
Status Public on Dec 17, 2005
Title RA LUMC-42 LC14n106 vs LCR syn tis
Sample type RNA
 
Channel 1
Source name RA mRNA
Organism Homo sapiens
Characteristics RA mRNA
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name LCR
Organism Homo sapiens
Characteristics LCR
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Diseased tissue, Rheumatoid arthritis
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10526.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
1 179 200 62 104 117 96 null null 63 119 null null null null null null null null 100 75 null null null null 1.219 .821 null null 1.101 null 12 104 .176 .21 null null null 109 114 82 87 0 309 161 148 1.268 null null .789 null .342 null
2 726 594 60 112 666 482 null null 62 119 null null null null null null null null 98 95 null null null null 1.382 .724 null null .688 null 120 612 .734 .92 null null null 107 119 96 108 0 918 173 745 1.118 null null .894 null .161 null
3 238 206 58 115 180 91 null null 62 125 null null null null null null null null 100 62 null null null null 1.978 .506 null null .47 null 32 236 .414 .47 null null null 107 114 117 124 0 318 178 141 .781 null null 1.28 null -.357 null
4 557 333 59 112 498 221 null null 61 128 null null null null null null null null 100 90 null null null null 2.253 .444 null null .423 null 52 322 .374 .69 null null null 107 115 133 141 0 514 173 341 .686 null null 1.459 null -.545 null
5 4126 10161 63 119 4063 10042 null null 64 130 null null null null null null null null 100 100 null null null null .405 2.472 null null 2.491 null 80 464 2.413 .96 null null null 106 116 149 159 0 15697 184 15513 3.818 null null .262 null 1.933 null
6 655 587 62 124 593 463 null null 63 134 null null null null null null null null 100 100 null null null null 1.281 .781 null null .774 null 52 320 .724 .88 null null null 107 115 167 175 0 907 192 715 1.206 null null .829 null .27 null
7 2894 1613 62 120 2832 1493 null null 69 130 null null null null null null null null 100 98 null null null null 1.897 .527 null null .494 null 80 529 .524 .9 null null null 105 116 183 194 0 2492 185 2306 .814 null null 1.228 null -.296 null
8 843 522 64 121 779 401 null null 80 133 null null null null null null null null 93 90 null null null null 1.943 .515 null null .566 null 32 231 .504 .89 null null null 108 115 201 208 0 806 187 619 .795 null null 1.258 null -.331 null
9 1794 1595 63 129 1731 1466 null null 71 135 null null null null null null null null 100 100 null null null null 1.181 .847 null null .833 null 80 592 .868 .93 null null null 103 114 218 229 0 2464 199 2265 1.308 null null .764 null .388 null
10 816 725 61 123 755 602 null null 151 529 null null null null null null null null 88 0 null null null null 1.254 .797 null null .772 null 52 316 3.583 .92 null null null 107 115 239 247 0 1120 190 930 1.232 null null .812 null .301 null
11 555 485 61 123 494 362 null null 64 131 null null null null null null null null 100 95 null null null null 1.365 .733 null null .636 null 80 515 .696 .79 null null null 103 114 254 265 0 749 190 559 1.132 null null .883 null .179 null
12 1915 1448 61 117 1854 1331 null null 66 123 null null null null null null null null 100 100 null null null null 1.393 .718 null null .653 null 120 605 .766 .95 null null null 105 117 272 284 0 2237 181 2056 1.109 null null .902 null .149 null
13 629 559 62 116 567 443 null null 70 124 null null null null null null null null 100 98 null null null null 1.28 .781 null null .739 null 80 418 .738 .85 null null null 105 115 289 299 0 864 179 684 1.207 null null .829 null .271 null
14 249 303 63 125 186 178 null null 71 135 null null null null null null null null 97 83 null null null null 1.045 .957 null null .943 null 120 687 .848 .67 null null null 103 116 307 320 0 468 193 275 1.478 null null .676 null .564 null
15 280 255 61 133 219 122 null null 69 143 null null null null null null null null 96 65 null null null null 1.795 .557 null null .642 null 80 400 .591 .65 null null null 105 115 324 334 -100 394 205 188 .861 null null 1.162 null -.217 null
16 1806 1714 60 125 1746 1589 null null 66 132 null null null null null null null null 100 100 null null null null 1.099 .91 null null .853 null 120 648 .921 .94 null null null 104 117 341 354 0 2648 193 2455 1.406 null null .711 null .491 null
17 182 226 60 125 122 101 null null 67 137 null null null null null null null null 87 56 null null null null 1.208 .828 null null .891 null 156 679 .586 .47 null null null 103 117 360 374 0 349 193 156 1.279 null null .782 null .355 null
18 164 210 61 124 103 86 null null 65 136 null null null null null null null null 64 46 null null null null 1.198 .835 null null .911 null 156 614 .932 .74 null null null 104 118 378 392 -100 324 192 133 1.29 null null .775 null .367 null
19 160 241 60 118 100 123 null null 61 126 null null null null null null null null 95 77 null null null null .813 1.23 null null 1.283 null 120 454 .873 .54 null null null 106 118 395 407 0 372 182 190 1.9 null null .526 null .926 null
20 444 347 60 123 384 224 null null 65 130 null null null null null null null null 100 83 null null null null 1.714 .583 null null .619 null 156 862 .547 .8 null null null 103 118 411 426 0 536 190 346 .901 null null 1.11 null -.15 null

Total number of rows: 18432

Table truncated, full table size 4364 Kbytes.




Supplementary data files not provided
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