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Sample GSM90613 Query DataSets for GSM90613
Status Public on Jan 05, 2006
Title T-lymphoblast vs. UHRR
Sample type RNA
 
Channel 1
Source name 20 ug total UHRR RNA labeled with amino allyl
Organism Homo sapiens
Characteristics 20 ug total UHRR RNA labeled with amino allyl
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 20 ug total T-lymphoblast cell line RNA labeled with amino allyl
Organism Homo sapiens
Characteristics 20 ug total T-lymphoblast cell line RNA labeled with amino allyl
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Reference verification, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24746.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 04, 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 GPL3305
Series (2)
GSE3972 Contribution of unique genes by individual cell lines to Universal Human Reference RNA
GSE4389 Universal Reference RNA as a standard for microarray experiments

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
1 312 393 95 40 217 353 316 378 96 42 221 338 0 0 121 168 23 16 93 100 90 97 570 559 .615 1.627 1.529 1.655 1.549 2.054 80 412 1.618 .85 100 1620 9070 97 107 93 103 0 247 25 222 1.023 238 213 .977 .962 .033 -.056
2 360 412 92 40 268 372 351 410 93 42 259 370 0 0 122 147 21 18 100 100 100 100 640 629 .72 1.388 1.429 1.402 1.358 1.701 52 280 1.424 .85 90 1760 9060 96 105 107 116 0 259 25 234 .873 258 233 1.145 .898 -.196 -.154
3 987 1298 97 40 890 1258 999 1347 99 41 902 1307 0 0 242 313 23 13 100 100 100 100 2148 2209 .707 1.413 1.449 1.424 1.401 1.313 52 325 1.447 .93 90 1900 9060 96 105 121 130 0 816 25 791 .889 847 822 1.125 .911 -.17 -.134
4 705 648 95 39 610 609 707 682 97 43 612 643 0 0 274 252 25 15 100 100 98 100 1219 1255 1.002 .998 1.051 1.04 1.027 1.756 52 328 .973 .91 90 2050 9070 97 106 136 145 0 408 25 383 .628 429 404 1.593 .661 -.671 -.598
5 288 222 94 41 194 181 290 200 96 45 196 159 0 0 91 90 24 17 96 100 96 96 375 355 1.072 .933 .811 .909 1.006 2.25 32 212 .97 .77 70 2190 9060 97 104 151 158 0 140 26 114 .587 126 100 1.704 .51 -.769 -.971
6 324 334 96 39 228 295 305 291 96 42 209 252 0 0 104 147 23 13 100 100 96 100 523 461 .773 1.294 1.206 1.292 1.363 2.137 32 228 1.35 .72 70 2340 9070 98 105 166 173 0 210 25 186 .814 183 158 1.229 .758 -.297 -.399
7 330 399 94 43 236 356 298 364 102 53 204 321 0 0 124 144 46 50 100 100 87 100 592 525 .663 1.508 1.574 1.634 1.481 1.774 32 221 1.436 .78 70 2480 9060 97 104 180 187 0 251 27 224 .949 229 202 1.054 .99 -.076 -.015
8 3933 5687 97 41 3836 5646 4093 6157 102 46 3996 6116 0 0 1813 3181 36 31 100 100 100 98 9482 10112 .679 1.472 1.531 1.272 1.471 1.983 80 404 1.625 .9 100 2640 9070 97 107 195 205 0 3577 26 3551 .926 3872 3847 1.08 .963 -.111 -.055
9 317 304 97 40 220 264 305 290 98 42 208 250 0 0 123 137 23 12 92 100 90 100 484 458 .833 1.2 1.202 1.288 1.31 2.226 52 317 1.191 .8 90 2770 9070 97 106 208 217 0 191 25 166 .755 182 157 1.325 .756 -.406 -.404
10 257 238 96 42 161 196 256 230 98 44 160 188 0 0 87 106 21 12 96 100 93 100 357 348 .821 1.217 1.175 1.15 1.065 2.189 32 204 1.275 .69 70 2930 9070 98 105 225 232 0 150 26 123 .766 145 118 1.306 .739 -.385 -.436
11 1028 1039 96 40 932 999 987 1003 97 41 891 963 0 0 403 460 23 11 100 100 100 100 1931 1854 .933 1.072 1.081 1.03 1.127 1.847 80 367 1.099 .9 100 3070 9070 97 107 238 248 0 653 25 628 .674 631 606 1.483 .68 -.569 -.557
12 471 509 95 40 376 469 478 488 94 41 383 448 0 0 192 227 23 11 98 100 96 100 845 831 .802 1.247 1.17 1.243 1.329 1.749 52 222 1.182 .82 80 3210 9080 99 107 253 261 0 320 25 295 .784 307 282 1.275 .736 -.35 -.443
13 292 290 94 40 198 250 272 267 95 41 178 227 0 0 137 187 23 10 93 97 81 95 448 405 .792 1.263 1.275 1.282 1.301 2.539 80 360 1.339 .82 100 3360 9070 97 107 267 277 0 182 25 157 .794 168 143 1.259 .802 -.333 -.318
14 199 147 93 41 106 106 181 137 95 43 88 96 0 0 76 71 23 13 86 94 75 84 212 184 1 1 1.091 1.03 1.056 2.674 52 251 .143 .31 80 3500 9070 98 106 282 290 0 92 26 67 .629 86 60 1.59 .686 -.669 -.543
15 1721 1491 91 40 1630 1451 1709 1557 94 42 1618 1517 0 0 506 553 24 12 100 100 100 100 3081 3135 1.123 .89 .938 .845 .895 1.544 80 398 .907 .92 100 3650 9070 97 107 296 306 0 938 25 913 .56 979 954 1.786 .59 -.837 -.762
16 512 489 88 39 424 450 515 519 90 41 427 480 0 0 122 105 22 12 98 100 98 100 874 907 .942 1.061 1.124 1.036 1.067 1.535 52 237 1.012 .88 80 3790 9080 99 107 311 319 0 308 25 283 .667 326 302 1.498 .707 -.583 -.5
17 333 282 91 43 242 239 312 289 95 49 221 246 0 0 120 93 28 26 100 100 96 100 481 467 1.013 .988 1.113 1.037 .973 1.748 32 214 .859 .7 70 3930 9060 97 104 325 332 0 177 27 150 .621 182 155 1.61 .7 -.687 -.514
18 238 225 94 41 144 184 229 232 97 44 135 191 0 0 83 88 25 20 96 98 90 98 328 326 .783 1.278 1.415 1.26 1.263 1.895 52 275 1.253 .76 80 4080 9070 98 106 340 348 0 142 26 116 .804 146 120 1.244 .89 -.315 -.168
19 619 507 95 40 524 467 615 503 97 42 520 463 0 0 197 190 22 18 100 100 100 100 991 983 1.122 .891 .89 .876 .823 1.59 80 384 .893 .91 100 4230 9070 97 107 354 364 0 319 25 294 .561 316 291 1.784 .56 -.835 -.837
20 341 354 96 43 245 311 317 342 98 47 221 299 0 0 99 102 23 20 96 100 96 100 556 520 .788 1.269 1.353 1.34 1.214 1.855 32 191 1.185 .85 70 4370 9070 98 105 369 376 0 223 27 196 .798 215 188 1.253 .851 -.325 -.233

Total number of rows: 43008

Table truncated, full table size 9295 Kbytes.




Supplementary data files not provided
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