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Sample GSM87755 Query DataSets for GSM87755
Status Public on Dec 15, 2005
Title RA LUMC-12 shr128 vs CRE 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 CRE
Organism Homo sapiens
Characteristics CRE
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Diseased tissue, Rheumatoid arthritis
Image: http://smd.stanford.edu/MicroArray/gifs//10444.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 GPL2831
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
1 687 587 242 315 445 272 null null 256 317 null null null null null null null null 100 100 null null null null 1.636 .611 null null .662 null 32 204 .438 .76 null null null 53 60 52 59 0 741 398 343 .771 null null 1.296 null -.374 null
2 294 295 249 314 45 -19 null null 262 316 null null null null null null null null 26 11 null null null null null null null null .741 null 80 497 .067 .11 null null null 50 61 65 76 0 372 396 -24 null null null null null null null
3 1440 1314 250 305 1190 1009 null null 269 311 null null null null null null null null 98 100 null null null null 1.179 .848 null null .87 null 52 274 .777 .92 null null null 53 61 82 90 0 1658 385 1273 1.07 null null .934 null .098 null
4 1115 799 254 289 861 510 null null 266 297 null null null null null null null null 100 100 null null null null 1.688 .592 null null .655 null 32 204 .496 .83 null null null 53 60 97 104 0 1008 365 644 .748 null null 1.338 null -.42 null
5 868 816 254 289 614 527 null null 264 292 null null null null null null null null 100 94 null null null null 1.165 .858 null null .89 null 52 263 .716 .84 null null null 53 61 112 120 0 1030 365 665 1.083 null null .923 null .115 null
6 339 239 263 289 76 -50 null null 290 297 null null null null null null null null 26 3 null null null null null null null null 1.294 null 80 448 .02 .03 null null null 50 61 124 135 0 302 365 -63 null null null null null null null
7 352 264 246 289 106 -25 null null 273 297 null null null null null null null null 35 3 null null null null null null null null .378 null 80 458 .226 .49 null null null 50 61 139 150 -100 333 365 -32 null null null null null null null
8 488 360 219 268 269 92 null null 235 272 null null null null null null null null 94 65 null null null null 2.924 .342 null null .43 null 52 284 .261 .51 null null null 53 61 157 165 0 454 338 116 .432 null null 2.317 null -1.212 null
9 417 287 191 242 226 45 null null 205 243 null null null null null null null null 93 46 null null null null 5.022 .199 null null .316 null 32 176 .116 .24 null null null 54 60 173 179 0 362 305 57 .251 null null 3.979 null -1.993 null
10 581 965 207 239 374 726 null null 221 246 null null null null null null null null 100 100 null null null null .515 1.941 null null 2.102 null 32 232 1.228 .78 null null null 52 59 186 193 0 1218 302 916 2.45 null null .408 null 1.293 null
11 464 363 205 229 259 134 null null 214 231 null null null null null null null null 96 87 null null null null 1.933 .517 null null .576 null 32 232 .321 .59 null null null 53 60 201 208 0 458 289 169 .653 null null 1.531 null -.615 null
12 573 474 206 220 367 254 null null 214 223 null null null null null null null null 100 100 null null null null 1.445 .692 null null .669 null 32 232 .482 .72 null null null 52 59 217 224 0 598 278 321 .873 null null 1.145 null -.195 null
13 435 455 200 207 235 248 null null 207 213 null null null null null null null null 90 100 null null null null .948 1.055 null null 1.129 null 32 228 .645 .66 null null null 53 60 231 238 0 574 261 313 1.332 null null .751 null .413 null
14 557 644 200 215 357 429 null null 210 214 null null null null null null null null 100 100 null null null null .832 1.202 null null 1.199 null 32 232 .947 .82 null null null 52 59 247 254 0 813 271 541 1.517 null null .659 null .601 null
15 438 648 205 225 233 423 null null 213 226 null null null null null null null null 90 100 null null null null .551 1.815 null null 1.663 null 32 220 .966 .69 null null null 52 59 261 268 0 818 284 534 2.291 null null .436 null 1.196 null
16 1428 1800 203 217 1225 1583 null null 213 221 null null null null null null null null 100 100 null null null null .774 1.292 null null 1.34 null 52 276 1.207 .93 null null null 52 60 276 284 0 2272 274 1998 1.631 null null .613 null .706 null
17 1418 1481 189 212 1229 1269 null null 199 216 null null null null null null null null 100 100 null null null null .968 1.033 null null 1.021 null 32 210 .945 .95 null null null 52 59 291 298 0 1869 268 1602 1.303 null null .767 null .382 null
18 594 541 204 216 390 325 null null 217 222 null null null null null null null null 98 100 null null null null 1.2 .833 null null .848 null 52 263 .615 .76 null null null 52 60 307 315 0 683 273 410 1.052 null null .951 null .073 null
19 266 187 205 210 61 -23 null null 215 215 null null null null null null null null 38 6 null null null null null null null null .5 null 80 459 .059 .1 null null null 49 60 319 330 -100 236 265 -29 null null null null null null null
20 383 329 202 208 181 121 null null 214 211 null null null null null null null null 75 84 null null null null 1.496 .669 null null .744 null 32 211 .242 .38 null null null 52 59 337 344 0 415 263 153 .844 null null 1.185 null -.245 null

Total number of rows: 24192

Table truncated, full table size 5828 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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