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Sample GSM93175 Query DataSets for GSM93175
Status Public on Jan 19, 2006
Title RA LB-3 sht005 CRE -cyt
Sample type RNA
 
Channel 1
Source name CRE
Organism Homo sapiens
Characteristics CRE
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name RA mRNA
Organism Homo sapiens
Characteristics RA mRNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-line, Rheumatoid arthritis
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11182.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 Jan 18, 2006
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 GPL2649
Series (1)
GSE4061 Fibroblast-like synoviocytes derived from patients with rheumatoid arthritis

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
1 356 284 89 183 267 101 null null 223 251 null null null null null null null null 28 10 null null null null 2.644 .378 null null .417 null 80 408 .423 .72 null null null 79 89 102 112 0 266 172 95 .355 null null 2.819 null -1.495 null
2 84 168 83 177 1 -9 null null 143 214 null null null null null null null null 0 1 null null null null null null null null 2.577 null 80 361 .593 .33 null null null 79 89 117 127 0 158 166 -8 null null null null null null null
3 75 171 77 179 -2 -8 null null 150 226 null null null null null null null null 0 1 null null null null null null null null 4.05 null 80 367 .786 .72 null null null 79 89 132 142 0 160 168 -8 null null null null null null null
4 848 843 88 204 760 639 null null 352 414 null null null null null null null null 73 65 null null null null 1.189 .841 null null .769 null 80 327 .801 .87 null null null 79 89 147 157 0 791 191 599 .789 null null 1.268 null -.343 null
5 827 1031 97 212 730 819 null null 415 522 null null null null null null null null 62 60 null null null null .891 1.122 null null 1.159 null 80 323 .971 .91 null null null 79 89 161 171 0 967 199 768 1.052 null null .95 null .073 null
6 76 189 77 174 -1 15 null null 208 323 null null null null null null null null 1 2 null null null null null null null null 2.648 null 80 353 1.154 .92 null null null 79 89 176 186 0 177 163 14 null null null null null null null
7 352 294 70 169 282 125 null null 76 174 null null null null null null null null 90 71 null null null null 2.256 .443 null null .552 null 52 242 .306 .49 null null null 80 88 191 199 0 276 158 117 .416 null null 2.405 null -1.266 null
8 438 332 70 168 368 164 null null 78 171 null null null null null null null null 96 80 null null null null 2.244 .446 null null .436 null 52 280 .361 .65 null null null 80 88 206 214 0 311 158 154 .418 null null 2.393 null -1.259 null
9 2279 1309 73 165 2206 1144 null null 79 171 null null null null null null null null 98 100 null null null null 1.928 .519 null null .496 null 52 305 .46 .91 null null null 79 88 222 231 0 1228 155 1073 .486 null null 2.056 null -1.04 null
10 215 215 76 160 139 55 null null 89 168 null null null null null null null null 81 40 null null null null 2.527 .396 null null .631 null 32 187 .125 .15 null null null 80 87 234 241 0 202 150 52 .371 null null 2.695 null -1.43 null
11 411 413 70 165 341 248 null null 77 171 null null null null null null null null 98 96 null null null null 1.375 .727 null null .736 null 52 344 .619 .75 null null null 79 88 251 260 0 387 155 233 .682 null null 1.466 null -.552 null
12 1867 468 67 169 1800 299 null null 72 179 null null null null null null null null 100 98 null null null null 6.02 .166 null null .173 null 52 289 .146 .8 null null null 79 88 266 275 0 439 158 280 .156 null null 6.419 null -2.682 null
13 822 1004 68 159 754 845 null null 73 174 null null null null null null null null 82 92 null null null null .892 1.121 null null 1.125 null 52 301 .886 .85 null null null 78 87 280 289 0 942 149 792 1.051 null null .951 null .072 null
14 9037 4647 70 152 8967 4495 null null 81 166 null null null null null null null null 100 100 null null null null 1.995 .501 null null .511 null 52 301 .451 .94 null null null 78 87 295 304 0 4358 143 4216 .47 null null 2.127 null -1.089 null
15 447 546 67 157 380 389 null null 79 168 null null null null null null null null 90 98 null null null null .977 1.024 null null .938 null 52 326 .758 .79 null null null 78 87 309 318 0 512 147 365 .96 null null 1.042 null -.059 null
16 1337 447 66 160 1271 287 null null 71 174 null null null null null null null null 96 96 null null null null 4.429 .226 null null .24 null 52 262 .182 .78 null null null 79 87 326 334 0 419 150 269 .212 null null 4.722 null -2.239 null
17 3691 7660 66 169 3625 7491 null null 72 184 null null null null null null null null 96 96 null null null null .484 2.066 null null 2.014 null 80 399 1.786 .93 null null null 78 88 340 350 0 7184 158 7025 1.938 null null .516 null .955 null
18 210 243 67 169 143 74 null null 78 186 null null null null null null null null 84 38 null null null null 1.932 .517 null null .804 null 52 238 .264 .21 null null null 78 86 356 364 0 228 158 69 .485 null null 2.06 null -1.043 null
19 2466 2264 65 170 2401 2094 null null 73 192 null null null null null null null null 90 92 null null null null 1.147 .872 null null .901 null 52 301 .733 .92 null null null 77 86 369 378 0 2123 159 1964 .818 null null 1.223 null -.29 null
20 562 591 67 164 495 427 null null 71 170 null null null null null null null null 92 90 null null null null 1.159 .863 null null 1.02 null 52 337 .718 .79 null null null 77 86 384 393 0 554 154 400 .809 null null 1.236 null -.306 null

Total number of rows: 24192

Table truncated, full table size 5756 Kbytes.




Supplementary data files not provided
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