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Sample GSM90616 Query DataSets for GSM90616
Status Public on Jan 05, 2006
Title Testis 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 testis cell line RNA labeled with amino allyl
Organism Homo sapiens
Characteristics 20 ug total testis 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/2002-01/24756.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
1 572 680 97 50 475 630 501 543 98 53 404 493 0 0 250 328 23 20 98 100 98 100 1105 897 .754 1.326 1.22 1.368 1.28 1.521 52 280 1.343 .95 80 1690 9110 83 91 85 93 0 540 40 500 1.053 431 391 .95 .968 .074 -.046
2 468 496 95 50 373 446 428 470 99 53 333 420 0 0 173 171 25 19 100 100 96 100 819 753 .836 1.196 1.261 1.267 1.224 1.562 52 244 18.398 .2 80 1830 9100 82 90 99 107 0 394 40 354 .949 373 333 1.054 1.001 -.076 .001
3 1612 2168 100 52 1512 2116 1689 2284 108 56 1589 2232 0 0 303 497 55 30 100 100 100 100 3628 3821 .715 1.399 1.405 1.385 1.404 1.195 52 324 1.424 .98 90 1980 9100 81 90 113 122 0 1721 41 1679 1.111 1813 1771 .9 1.115 .151 .157
4 1689 2817 103 52 1586 2765 1792 2999 108 57 1689 2947 0 0 767 1161 48 25 100 100 100 100 4351 4636 .574 1.743 1.745 1.839 1.723 1.477 52 259 1.715 .97 80 2130 9110 83 91 129 137 0 2236 41 2194 1.384 2380 2339 .723 1.385 .468 .47
5 540 649 105 50 435 599 465 516 107 53 360 466 0 0 247 404 23 16 100 100 100 100 1034 826 .726 1.377 1.294 1.289 1.318 1.49 32 203 1.502 .93 70 2270 9100 82 89 143 150 0 515 40 475 1.093 410 370 .915 1.027 .128 .039
6 537 716 109 53 428 663 446 545 118 59 337 492 0 0 339 491 86 47 93 100 78 96 1091 829 .646 1.549 1.46 1.577 1.513 1.767 32 226 1.53 .95 70 2420 9110 83 90 158 165 0 568 42 526 1.229 433 390 .813 1.159 .298 .212
7 601 785 107 58 494 727 428 686 122 67 321 628 0 0 329 416 96 57 100 100 90 100 1221 949 .68 1.472 1.956 1.517 1.507 1.439 32 210 1.387 .94 70 2560 9100 82 89 172 179 0 623 46 577 1.168 544 498 .856 1.553 .224 .635
8 6922 14783 109 58 6813 14725 6809 15168 127 85 6700 15110 0 0 2110 4501 186 223 100 100 100 100 21538 21810 .463 2.161 2.255 2.149 2.036 1.238 52 337 2.153 .98 90 2710 9100 81 90 186 195 0 11733 46 11687 1.715 12038 11992 .583 1.79 .778 .84
9 682 717 109 56 573 661 660 616 122 73 551 560 0 0 257 330 161 183 98 98 84 80 1234 1111 .867 1.154 1.016 1.129 1.1 1.445 52 267 1.18 .93 80 2860 9110 83 91 202 210 0 569 44 525 .916 489 444 1.092 .807 -.127 -.31
10 413 520 103 56 310 464 384 467 105 58 281 411 0 0 212 333 29 19 96 100 96 100 774 692 .668 1.497 1.463 1.445 1.471 1.441 32 207 1.504 .95 70 3010 9120 84 91 217 224 0 413 44 368 1.188 371 326 .842 1.161 .248 .215
11 2113 4108 99 54 2014 4054 2128 4373 104 60 2029 4319 0 0 663 966 30 27 100 100 100 100 6068 6348 .497 2.013 2.129 2.046 2.086 1.355 52 324 1.868 .75 90 3150 9110 82 91 230 239 0 3260 43 3217 1.598 3471 3428 .626 1.689 .676 .757
12 986 2384 97 58 889 2326 962 2204 104 91 865 2146 0 0 404 826 53 239 100 100 100 100 3215 3011 .382 2.616 2.481 2.705 2.748 1.272 32 207 2.612 .95 70 3290 9110 83 90 245 252 0 1892 46 1846 2.077 1749 1703 .482 1.969 1.054 .977
13 583 844 98 53 485 791 506 769 107 93 408 716 0 0 276 403 53 214 98 100 96 82 1276 1124 .613 1.631 1.755 1.735 1.662 1.471 52 277 2.31 .76 80 3440 9110 83 91 260 268 0 670 42 628 1.294 610 568 .773 1.393 .372 .478
14 420 406 100 56 320 350 372 344 101 59 272 288 0 0 182 272 26 25 100 100 100 96 670 560 .914 1.094 1.059 .943 1.002 1.735 32 165 1.263 .89 60 3590 9120 85 91 276 282 0 322 44 278 .868 273 229 1.152 .84 -.204 -.251
15 3634 5905 100 54 3534 5851 3603 5995 102 58 3503 5941 0 0 899 1284 28 22 100 100 100 100 9385 9444 .604 1.656 1.696 1.68 1.597 1.174 52 332 1.652 .98 90 3730 9120 83 92 288 297 0 4687 43 4644 1.314 4758 4715 .761 1.346 .394 .429
16 902 1319 97 51 805 1268 857 1284 101 54 760 1233 0 0 255 343 28 19 100 100 100 100 2073 1993 .635 1.575 1.622 1.596 1.59 1.28 52 264 1.579 .95 80 3880 9120 84 92 304 312 0 1047 40 1006 1.25 1019 979 .8 1.288 .322 .365
17 389 506 98 52 291 454 328 428 100 57 230 376 0 0 188 296 26 20 98 100 96 100 745 606 .641 1.56 1.635 1.563 1.546 1.65 52 275 1.567 .93 80 4020 9110 83 91 318 326 0 402 41 360 1.238 340 298 .808 1.297 .308 .376
18 306 306 103 60 203 246 292 254 106 64 189 194 0 0 91 139 31 24 96 100 96 100 449 383 .825 1.212 1.026 1.244 1.172 1.736 32 219 1.236 .89 70 4170 9110 83 90 333 340 -100 243 48 195 .962 202 154 1.04 .815 -.056 -.296
19 960 1381 135 80 825 1301 944 1363 150 98 809 1283 0 0 241 394 75 78 100 100 100 100 2126 2092 .634 1.577 1.586 1.564 1.56 1.306 52 341 1.575 .95 90 4320 9100 81 90 347 356 -100 1096 63 1033 1.252 1082 1018 .799 1.259 .324 .332
20 623 756 107 62 516 694 617 775 111 67 510 713 0 0 202 274 30 27 100 100 100 100 1210 1223 .744 1.345 1.398 1.337 1.3 1.347 32 165 1.363 .95 60 4470 9120 85 91 364 370 -100 600 49 551 1.067 615 566 .937 1.11 .094 .15

Total number of rows: 43008

Table truncated, full table size 9226 Kbytes.




Supplementary data files not provided
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