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Sample GSM87765 Query DataSets for GSM87765
Status Public on Dec 15, 2005
Title RA LUMC-53 shab101 vs CRD
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/2000-10/10554.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 1307 1676 45 68 1262 1608 null null 45 73 null null null null null null null null 100 100 null null null null .785 1.274 null null 1.245 null 80 394 1.195 .95 null null null 90 100 100 110 0 1618 66 1552 1.23 null null .813 null .299 null
2 1751 2329 45 66 1706 2263 null null 46 72 null null null null null null null null 98 100 null null null null .754 1.326 null null 1.337 null 80 336 1.257 .94 null null null 90 100 115 125 0 2248 64 2185 1.281 null null .781 null .357 null
3 802 784 43 63 759 721 null null 45 68 null null null null null null null null 100 100 null null null null 1.053 .95 null null .921 null 80 385 .87 .93 null null null 90 100 131 141 0 757 61 696 .917 null null 1.09 null -.125 null
4 229 574 43 62 186 512 null null 45 72 null null null null null null null null 98 100 null null null null .363 2.753 null null 2.69 null 80 412 2.301 .87 null null null 89 100 146 157 0 554 60 494 2.657 null null .376 null 1.41 null
5 924 476 41 61 883 415 null null 43 64 null null null null null null null null 100 100 null null null null 2.128 .47 null null .475 null 80 412 .399 .86 null null null 89 100 160 171 0 460 59 401 .454 null null 2.204 null -1.14 null
6 892 908 43 64 849 844 null null 46 73 null null null null null null null null 100 100 null null null null 1.006 .994 null null .97 null 52 331 .925 .93 null null null 90 99 175 184 0 877 62 815 .96 null null 1.042 null -.059 null
7 500 569 44 64 456 505 null null 46 75 null null null null null null null null 100 100 null null null null .903 1.107 null null 1.175 null 32 232 .968 .91 null null null 92 99 192 199 0 549 62 488 1.069 null null .935 null .096 null
8 333 1458 44 65 289 1393 null null 45 72 null null null null null null null null 100 100 null null null null .207 4.82 null null 4.733 null 32 227 4.181 .9 null null null 92 99 206 213 0 1407 63 1345 4.653 null null .215 null 2.218 null
9 4522 1650 44 66 4478 1584 null null 45 70 null null null null null null null null 100 98 null null null null 2.827 .354 null null .359 null 52 291 .346 .94 null null null 92 100 222 230 0 1593 64 1529 .341 null null 2.928 null -1.55 null
10 826 218 45 67 781 151 null null 47 70 null null null null null null null null 100 100 null null null null 5.172 .193 null null .183 null 32 224 .181 .65 null null null 92 99 236 243 0 210 65 146 .187 null null 5.358 null -2.422 null
11 300 1109 44 66 256 1043 null null 45 69 null null null null null null null null 98 100 null null null null .245 4.074 null null 4.255 null 52 276 3.418 .91 null null null 93 101 253 261 0 1071 64 1007 3.933 null null .254 null 1.976 null
12 1247 606 43 65 1204 541 null null 43 70 null null null null null null null null 100 98 null null null null 2.226 .449 null null .448 null 52 264 .435 .93 null null null 93 101 267 275 0 585 63 522 .434 null null 2.305 null -1.205 null
13 1084 1611 43 65 1041 1546 null null 44 69 null null null null null null null null 100 100 null null null null .673 1.485 null null 1.476 null 80 363 1.303 .93 null null null 93 103 282 292 0 1555 63 1492 1.434 null null .698 null .52 null
14 5620 3145 44 65 5576 3080 null null 45 69 null null null null null null null null 100 100 null null null null 1.81 .552 null null .564 null 80 427 .534 .93 null null null 92 103 295 306 0 3036 63 2973 .533 null null 1.875 null -.907 null
15 413 799 46 59 367 740 null null 47 64 null null null null null null null null 100 100 null null null null .496 2.016 null null 2.038 null 52 264 1.914 .94 null null null 94 102 312 320 0 771 57 714 1.946 null null .514 null .961 null
16 717 379 46 53 671 326 null null 47 55 null null null null null null null null 100 98 null null null null 2.058 .486 null null .486 null 52 272 .459 .91 null null null 94 102 327 335 0 366 51 315 .469 null null 2.132 null -1.092 null
17 3689 5347 44 61 3645 5286 null null 53 79 null null null null null null null null 98 97 null null null null .69 1.45 null null 1.487 null 80 364 1.358 .93 null null null 94 104 341 351 0 5162 59 5103 1.4 null null .714 null .485 null
18 356 3705 42 61 314 3644 null null 43 65 null null null null null null null null 100 100 null null null null .086 11.605 null null 11.28 null 80 419 10.991 .93 null null null 93 104 355 366 0 3577 59 3518 11.203 null null .089 null 3.486 null
19 2868 1834 44 61 2824 1773 null null 90 418 null null null null null null null null 100 0 null null null null 1.593 .628 null null .653 null 52 283 .603 .92 null null null 95 103 372 380 0 1770 59 1712 .606 null null 1.65 null -.722 null
20 660 1593 45 62 615 1531 null null 82 356 null null null null null null null null 73 0 null null null null .402 2.489 null null 2.519 null 52 347 5.049 .66 null null null 95 104 387 396 0 1538 60 1478 2.403 null null .416 null 1.265 null

Total number of rows: 24192

Table truncated, full table size 5631 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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