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Sample GSM87752 Query DataSets for GSM87752
Status Public on Dec 15, 2005
Title RA LUMC-27 shab088a vs CRD 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 CRD
Organism Homo sapiens
Characteristics CRD
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Diseased tissue, Rheumatoid arthritis
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10514.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 GPL3007
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 1342 1134 51 170 1291 964 null null 58 184 null null null null null null null null 100 100 null null null null 1.339 .747 null null .709 null 80 451 .652 .83 null null null 75 86 65 76 0 1399 210 1190 .921 null null 1.085 null -.118 null
2 1284 1002 54 162 1230 840 null null 63 174 null null null null null null null null 100 100 null null null null 1.464 .683 null null .639 null 52 289 .556 .83 null null null 75 84 80 89 0 1236 200 1037 .843 null null 1.187 null -.247 null
3 985 505 53 165 932 340 null null 58 178 null null null null null null null null 100 91 null null null null 2.741 .365 null null .282 null 80 470 .338 .69 null null null 74 85 95 106 0 623 204 420 .45 null null 2.221 null -1.151 null
4 266 270 50 154 216 116 null null 55 168 null null null null null null null null 100 47 null null null null 1.862 .537 null null .448 null 80 384 .48 .48 null null null 76 86 112 122 0 333 190 143 .663 null null 1.509 null -.594 null
5 1169 511 50 148 1119 363 null null 56 165 null null null null null null null null 100 93 null null null null 3.083 .324 null null .295 null 80 396 .296 .76 null null null 75 85 127 137 0 631 183 448 .4 null null 2.498 null -1.321 null
6 995 572 53 161 942 411 null null 60 170 null null null null null null null null 100 98 null null null null 2.292 .436 null null .374 null 80 500 .404 .74 null null null 75 86 142 153 0 706 199 507 .538 null null 1.857 null -.893 null
7 1092 746 57 153 1035 593 null null 77 161 null null null null null null null null 100 91 null null null null 1.745 .573 null null .663 null 12 93 .567 .79 null null null 77 82 158 163 0 921 189 732 .707 null null 1.414 null -.5 null
8 624 1165 58 162 566 1003 null null 64 168 null null null null null null null null 94 100 null null null null .564 1.772 null null 2.235 null 52 299 1.23 .84 null null null 78 86 173 181 0 1438 200 1238 2.187 null null .457 null 1.129 null
9 6828 1023 54 154 6774 869 null null 59 167 null null null null null null null null 100 98 null null null null 7.795 .128 null null .117 null 52 264 .126 .86 null null null 78 86 188 196 0 1262 190 1072 .158 null null 6.317 null -2.659 null
10 1010 294 51 143 959 151 null null 57 157 null null null null null null null null 100 56 null null null null 6.351 .157 null null .199 null 52 281 .174 .65 null null null 78 86 202 210 0 363 176 186 .194 null null 5.147 null -2.364 null
11 486 868 49 137 437 731 null null 54 155 null null null null null null null null 100 98 null null null null .598 1.673 null null 1.566 null 52 291 1.419 .85 null null null 78 86 218 226 0 1071 169 902 2.064 null null .484 null 1.046 null
12 1931 360 45 130 1886 230 null null 49 145 null null null null null null null null 100 84 null null null null 8.2 .122 null null .119 null 52 310 .113 .7 null null null 77 86 232 241 0 444 160 284 .15 null null 6.645 null -2.732 null
13 1186 879 48 131 1138 748 null null 52 145 null null null null null null null null 98 98 null null null null 1.521 .657 null null .665 null 80 364 .573 .85 null null null 78 88 246 256 0 1085 162 923 .811 null null 1.233 null -.302 null
14 5337 1037 46 126 5291 911 null null 51 134 null null null null null null null null 100 95 null null null null 5.808 .172 null null .164 null 80 394 .158 .86 null null null 78 88 261 271 0 1280 155 1124 .212 null null 4.707 null -2.235 null
15 351 330 42 112 309 218 null null 45 121 null null null null null null null null 100 94 null null null null 1.417 .706 null null .63 null 52 272 .613 .69 null null null 79 87 277 285 0 407 138 269 .871 null null 1.149 null -.2 null
16 918 330 43 123 875 207 null null 48 126 null null null null null null null null 100 90 null null null null 4.227 .237 null null .226 null 52 270 .211 .75 null null null 79 87 293 301 0 407 152 255 .292 null null 3.426 null -1.776 null
17 2734 1025 43 126 2691 899 null null 49 137 null null null null null null null null 100 100 null null null null 2.993 .334 null null .329 null 80 350 .309 .91 null null null 79 89 306 316 0 1265 155 1109 .412 null null 2.426 null -1.278 null
18 356 1379 43 124 313 1255 null null 49 138 null null null null null null null null 98 100 null null null null .249 4.01 null null 4.119 null 80 389 3.379 .87 null null null 79 89 320 330 0 1702 153 1549 4.948 null null .202 null 2.307 null
19 2822 824 48 128 2774 696 null null 52 139 null null null null null null null null 100 98 null null null null 3.986 .251 null null .276 null 52 285 .227 .87 null null null 80 88 337 345 0 1017 158 859 .31 null null 3.23 null -1.691 null
20 817 883 49 129 768 754 null null 54 141 null null null null null null null null 100 100 null null null null 1.019 .982 null null .826 null 52 283 1.004 .75 null null null 81 89 352 360 0 1090 159 930 1.211 null null .825 null .277 null

Total number of rows: 24192

Table truncated, full table size 5706 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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