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Sample GSM87762 Query DataSets for GSM87762
Status Public on Dec 15, 2005
Title RA LUMC-19 shab097 vs CRD syn tis
Sample type RNA
 
Channel 1
Source name CRD
Organism Homo sapiens
Characteristics CRD
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name RA LUMC-19 mRNA
Organism Homo sapiens
Characteristics RA LUMC-19 mRNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Diseased tissue, Rheumatoid arthritis
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11677.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 1477 1417 50 146 1427 1271 null null 52 156 null null null null null null null null 100 100 null null null null 1.123 .891 null null .911 null 52 337 .848 .93 null null null 64 73 66 75 0 1801 186 1616 1.132 null null .883 null .179 null
2 1158 1252 51 145 1107 1107 null null 54 155 null null null null null null null null 100 100 null null null null 1 1 null null 1.037 null 52 322 .95 .92 null null null 64 73 81 90 0 1591 184 1407 1.271 null null .787 null .346 null
3 999 484 52 135 947 349 null null 54 137 null null null null null null null null 100 100 null null null null 2.713 .369 null null .367 null 52 336 .372 .9 null null null 64 73 98 107 0 615 172 444 .468 null null 2.135 null -1.094 null
4 284 1293 52 134 232 1159 null null 55 157 null null null null null null null null 96 100 null null null null .2 4.996 null null 4.697 null 80 339 4.183 .89 null null null 65 75 113 123 0 1643 170 1473 6.35 null null .157 null 2.667 null
5 2141 338 67 283 2074 55 null null 69 293 null null null null null null null null 100 7 null null null null 37.709 .027 null null .032 null 52 289 .016 .1 null null null 65 74 127 136 0 430 360 70 .034 null null 29.667 null -4.891 null
6 1098 792 63 216 1035 576 null null 67 259 null null null null null null null null 100 100 null null null null 1.797 .557 null null .537 null 52 305 .5 .87 null null null 66 74 143 151 0 1007 275 732 .707 null null 1.414 null -.499 null
7 1034 633 54 134 980 499 null null 68 136 null null null null null null null null 100 100 null null null null 1.964 .509 null null .542 null 12 98 .496 .89 null null null 66 71 159 164 0 805 170 634 .647 null null 1.545 null -.628 null
8 576 1237 52 140 524 1097 null null 55 142 null null null null null null null null 100 100 null null null null .478 2.094 null null 2.367 null 32 225 1.454 .77 null null null 66 73 173 180 0 1572 178 1394 2.661 null null .376 null 1.412 null
9 5413 1261 53 151 5360 1110 null null 56 157 null null null null null null null null 100 92 null null null null 4.829 .207 null null .218 null 52 296 .197 .89 null null null 67 75 188 196 0 1603 192 1411 .263 null null 3.799 null -1.926 null
10 1073 286 52 136 1021 150 null null 55 142 null null null null null null null null 100 68 null null null null 6.807 .147 null null .114 null 32 225 .157 .69 null null null 66 73 203 210 0 364 173 191 .187 null null 5.355 null -2.421 null
11 464 1192 52 141 412 1051 null null 53 144 null null null null null null null null 100 100 null null null null .392 2.551 null null 2.566 null 52 282 2.053 .88 null null null 67 75 219 227 0 1515 179 1336 3.242 null null .308 null 1.697 null
12 2051 630 54 142 1997 488 null null 56 144 null null null null null null null null 100 96 null null null null 4.092 .244 null null .236 null 52 277 .247 .88 null null null 67 75 233 241 0 801 180 620 .311 null null 3.22 null -1.687 null
13 573 618 51 126 522 492 null null 80 147 null null null null null null null null 93 87 null null null null 1.061 .943 null null .874 null 32 210 .756 .77 null null null 67 74 246 253 0 786 160 625 1.198 null null .835 null .261 null
14 28 35 45 117 -17 -82 null null 261 141 null null null null null null null null 0 0 null null null null null null null null 3.776 null 80 466 .102 .69 null null null 66 76 262 272 -100 44 149 -104 null null null null null null null
15 505 741 51 132 454 609 null null 381 203 null null null null null null null null 0 87 null null null null .745 1.341 null null 1.37 null 32 210 .081 .37 null null null 67 74 277 284 0 942 168 774 1.705 null null .587 null .77 null
16 1270 462 50 113 1220 349 null null 53 122 null null null null null null null null 100 86 null null null null 3.496 .286 null null .287 null 52 307 .295 .88 null null null 68 76 294 302 0 587 144 444 .364 null null 2.75 null -1.46 null
17 4518 3740 51 110 4467 3630 null null 54 117 null null null null null null null null 100 100 null null null null 1.231 .813 null null .756 null 52 318 .833 .9 null null null 67 76 308 317 0 4754 140 4614 1.033 null null .968 null .047 null
18 417 1568 51 125 366 1443 null null 54 129 null null null null null null null null 100 100 null null null null .254 3.943 null null 4.111 null 80 412 3.568 .87 null null null 67 77 323 333 0 1993 159 1834 5.011 null null .2 null 2.325 null
19 3633 1881 54 144 3579 1737 null null 58 147 null null null null null null null null 100 94 null null null null 2.06 .485 null null .511 null 52 284 .482 .91 null null null 69 77 339 347 0 2391 183 2208 .617 null null 1.621 null -.697 null
20 900 798 53 143 847 655 null null 57 148 null null null null null null null null 100 100 null null null null 1.293 .773 null null .719 null 32 230 .758 .87 null null null 69 76 354 361 0 1014 182 833 .983 null null 1.017 null -.025 null

Total number of rows: 24192

Table truncated, full table size 5681 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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