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Sample GSM93173 Query DataSets for GSM93173
Status Public on Jan 19, 2006
Title RA LUMC-57 shr 129a 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//11180.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 GPL2831
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
1 201 248 88 203 113 45 null null 106 214 null null null null null null null null 83 16 null null null null 2.511 .398 null null .207 null 12 90 .144 .15 null null null 89 94 69 74 0 505 413 92 .811 null null 1.234 null -.303 null
2 107 206 84 196 23 10 null null 88 206 null null null null null null null null 37 18 null null null null 2.3 .435 null null 2.52 null 80 461 .226 .09 null null null 88 98 82 92 -100 419 399 20 .885 null null 1.13 null -.176 null
3 708 466 83 191 625 275 null null 87 208 null null null null null null null null 100 84 null null null null 2.273 .44 null null .356 null 32 218 .393 .66 null null null 90 97 98 105 0 949 389 560 .896 null null 1.117 null -.159 null
4 324 252 91 196 233 56 null null 92 198 null null null null null null null null 100 46 null null null null 4.161 .24 null null .513 null 32 224 .185 .22 null null null 89 96 113 120 0 513 399 114 .489 null null 2.044 null -1.031 null
5 343 284 87 189 256 95 null null 90 197 null null null null null null null null 100 53 null null null null 2.695 .371 null null .447 null 32 216 .343 .49 null null null 89 96 129 136 0 578 385 193 .755 null null 1.324 null -.405 null
6 129 189 83 183 46 6 null null 89 192 null null null null null null null null 55 18 null null null null 7.667 .13 null null 1.05 null 80 405 .145 .06 null null null 87 97 142 152 -100 385 372 12 .265 null null 3.767 null -1.913 null
7 125 197 84 190 41 7 null null 95 199 null null null null null null null null 38 20 null null null null 5.857 .171 null null 1.232 null 80 364 .233 .18 null null null 87 97 157 167 -100 401 387 14 .348 null null 2.878 null -1.525 null
8 138 209 83 187 55 22 null null 86 193 null null null null null null null null 61 22 null null null null 2.5 .4 null null .977 null 80 391 .207 .13 null null null 87 97 172 182 -100 425 381 45 .814 null null 1.228 null -.297 null
9 129 226 82 186 47 40 null null 86 192 null null null null null null null null 61 32 null null null null 1.175 .851 null null 1.129 null 80 389 .483 .25 null null null 87 97 187 197 -100 460 379 81 1.732 null null .577 null .793 null
10 132 223 80 194 52 29 null null 83 199 null null null null null null null null 68 22 null null null null 1.793 .558 null null .93 null 80 362 .463 .24 null null null 86 96 202 212 -100 454 395 59 1.135 null null .881 null .183 null
11 134 209 78 192 56 17 null null 80 196 null null null null null null null null 68 21 null null null null 3.294 .304 null null 1.145 null 80 333 .17 .1 null null null 86 96 217 227 -100 425 391 35 .618 null null 1.618 null -.695 null
12 145 211 80 193 65 18 null null 83 196 null null null null null null null null 65 25 null null null null 3.611 .277 null null .75 null 80 332 .162 .1 null null null 86 96 232 242 -100 429 393 37 .564 null null 1.774 null -.827 null
13 141 206 81 195 60 11 null null 84 200 null null null null null null null null 68 12 null null null null 5.455 .183 null null .714 null 80 385 .173 .09 null null null 86 96 247 257 -100 419 397 22 .373 null null 2.68 null -1.422 null
14 193 381 79 192 114 189 null null 83 195 null null null null null null null null 100 71 null null null null .603 1.658 null null 1.87 null 32 164 1.351 .58 null null null 88 94 265 271 0 776 391 385 3.375 null null .296 null 1.755 null
15 168 196 82 192 86 4 null null 87 197 null null null null null null null null 70 22 null null null null 21.5 .047 null null .673 null 80 429 -.03 -.03 null null null 85 95 277 287 -100 399 391 8 .095 null null 10.563 null -3.401 null
16 764 616 81 198 683 418 null null 86 206 null null null null null null null null 100 100 null null null null 1.634 .612 null null .596 null 32 214 .516 .81 null null null 86 93 294 301 0 1254 403 851 1.246 null null .803 null .317 null
17 578 372 82 191 496 181 null null 86 201 null null null null null null null null 100 87 null null null null 2.74 .365 null null .353 null 32 229 .286 .57 null null null 86 93 308 315 0 757 389 368 .743 null null 1.346 null -.429 null
18 236 249 75 189 161 60 null null 79 204 null null null null null null null null 100 46 null null null null 2.683 .373 null null .514 null 32 150 .384 .39 null null null 86 92 325 331 0 507 385 122 .759 null null 1.318 null -.399 null
19 85 193 73 178 12 15 null null 76 190 null null null null null null null null 35 16 null null null null .8 1.25 null null 2.5 null 80 377 .356 .11 null null null 84 94 336 346 -100 393 362 31 2.544 null null .393 null 1.347 null
20 116 207 72 181 44 26 null null 75 192 null null null null null null null null 70 26 null null null null 1.692 .591 null null 1.222 null 80 337 .2 .1 null null null 84 94 351 361 -100 421 368 53 1.203 null null .831 null .266 null

Total number of rows: 24192

Table truncated, full table size 5757 Kbytes.




Supplementary data files not provided
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