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Sample GSM93162 Query DataSets for GSM93162
Status Public on Jan 19, 2006
Title RA LUMC-25 shai033 vs CRE synoviocytes
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//10891.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 GPL3002
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 1285 533 61 70 1224 463 null null 62 73 null null null null null null null null 100 100 null null null null 2.644 .378 null null .373 null 52 288 .363 .95 null null null 58 66 62 70 0 1193 157 1036 .847 null null 1.181 null -.24 null
2 1787 951 62 71 1725 880 null null 64 74 null null null null null null null null 100 100 null null null null 1.96 .51 null null .505 null 52 275 .482 .96 null null null 59 67 78 86 0 2128 159 1970 1.142 null null .876 null .191 null
3 976 747 60 73 916 674 null null 62 77 null null null null null null null null 100 98 null null null null 1.359 .736 null null .757 null 52 266 .722 .95 null null null 59 67 93 101 0 1672 163 1508 1.647 null null .607 null .72 null
4 828 391 60 74 768 317 null null 62 76 null null null null null null null null 100 100 null null null null 2.423 .413 null null .394 null 52 268 .366 .92 null null null 59 67 108 116 0 875 166 709 .924 null null 1.082 null -.114 null
5 3401 2429 58 75 3343 2354 null null 61 76 null null null null null null null null 100 100 null null null null 1.42 .704 null null .708 null 52 269 .675 .97 null null null 59 67 123 131 0 5436 168 5268 1.576 null null .635 null .656 null
6 1647 651 61 74 1586 577 null null 62 75 null null null null null null null null 100 98 null null null null 2.749 .364 null null .367 null 52 341 .354 .95 null null null 58 67 137 146 0 1457 166 1291 .814 null null 1.228 null -.296 null
7 723 272 59 69 664 203 null null 61 73 null null null null null null null null 100 100 null null null null 3.271 .306 null null .307 null 32 225 .276 .9 null null null 58 65 153 160 0 609 154 454 .684 null null 1.461 null -.547 null
8 758 419 59 74 699 345 null null 62 77 null null null null null null null null 100 96 null null null null 2.026 .494 null null .493 null 52 274 .471 .95 null null null 59 67 169 177 0 938 166 772 1.105 null null .905 null .144 null
9 10508 2625 64 75 10444 2550 null null 66 83 null null null null null null null null 100 98 null null null null 4.096 .244 null null .24 null 52 256 .233 .96 null null null 59 67 183 191 0 5875 168 5707 .546 null null 1.83 null -.872 null
10 432 130 61 74 371 56 null null 63 78 null null null null null null null null 96 76 null null null null 6.625 .151 null null .15 null 52 274 .131 .62 null null null 59 67 198 206 0 291 166 125 .338 null null 2.96 null -1.566 null
11 1110 3337 59 73 1051 3264 null null 61 76 null null null null null null null null 98 100 null null null null .322 3.106 null null 2.974 null 52 344 2.891 .96 null null null 58 67 213 222 0 7468 163 7305 6.951 null null .144 null 2.797 null
12 3298 469 59 76 3239 393 null null 61 77 null null null null null null null null 100 100 null null null null 8.242 .121 null null .123 null 52 285 .119 .95 null null null 59 67 229 237 0 1050 170 880 .272 null null 3.682 null -1.881 null
13 2256 2235 61 74 2195 2161 null null 67 80 null null null null null null null null 100 100 null null null null 1.016 .985 null null .975 null 32 225 .903 .95 null null null 60 67 244 251 0 5002 166 4837 2.203 null null .454 null 1.14 null
14 15732 4831 64 75 15668 4756 null null 67 78 null null null null null null null null 100 98 null null null null 3.294 .304 null null .295 null 52 293 .3 .97 null null null 60 68 260 268 0 10812 168 10644 .679 null null 1.472 null -.558 null
15 1107 1811 64 80 1043 1731 null null 64 80 null null null null null null null null 100 100 null null null null .603 1.66 null null 1.663 null 52 264 1.54 .96 null null null 60 68 274 282 0 4053 179 3874 3.714 null null .269 null 1.893 null
16 3456 802 62 78 3394 724 null null 65 80 null null null null null null null null 100 96 null null null null 4.688 .213 null null .208 null 52 264 .207 .94 null null null 60 68 290 298 0 1795 175 1620 .477 null null 2.095 null -1.067 null
17 8951 11280 61 74 8890 11206 null null 63 79 null null null null null null null null 100 100 null null null null .793 1.261 null null 1.243 null 52 277 1.208 .96 null null null 60 68 304 312 0 25246 166 25080 2.821 null null .354 null 1.496 null
18 383 159 62 77 321 82 null null 63 79 null null null null null null null null 100 90 null null null null 3.915 .255 null null .211 null 32 224 .244 .72 null null null 60 67 319 326 0 356 172 184 .572 null null 1.749 null -.807 null
19 7469 3342 62 80 7407 3262 null null 63 84 null null null null null null null null 100 100 null null null null 2.271 .44 null null .434 null 52 294 .422 .95 null null null 60 68 334 342 0 7480 179 7301 .986 null null 1.015 null -.021 null
20 1452 1197 61 79 1391 1118 null null 63 81 null null null null null null null null 100 98 null null null null 1.244 .804 null null .812 null 52 283 .764 .95 null null null 60 68 350 358 0 2679 177 2502 1.799 null null .556 null .847 null

Total number of rows: 24192

Table truncated, full table size 5697 Kbytes.




Supplementary data files not provided
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