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Sample GSM90633 Query DataSets for GSM90633
Status Public on Jan 05, 2006
Title testis cell line
Sample type RNA
 
Channel 1
Source name stratagene mouse reference
Organism Mus musculus
Characteristics stratagene mouse reference
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name testis cell line
Organism Mus musculus
Characteristics testis cell line
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tissue, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20337.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 GPL3304
Series (2)
GSE3974 Contribution of unique genes by individual cell lines to Universal Mouse 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 2494 3095 112 267 2382 2828 2979 3441 123 295 2867 3174 0 0 1666 1980 61 191 82 81 79 76 5210 6041 .842 1.187 1.107 1.425 1.199 2.62 208 952 1.226 .92 160 2790 4050 49 65 71 87 0 3328 287 3041 1.277 3700 3413 .783 1.19 .352 .251
2 229 492 106 258 123 234 232 456 122 277 126 198 0 0 103 251 70 152 62 56 43 34 357 324 .526 1.902 1.571 2.137 2.169 2.861 208 689 4.307 .51 160 2970 4050 49 65 89 105 0 529 277 252 2.046 490 213 .489 1.69 1.033 .757
3 194 454 106 276 88 178 183 431 125 289 77 155 0 0 109 235 88 147 42 50 6 25 266 232 .494 2.023 2.013 2.524 2.494 3.133 208 626 5.107 .32 160 3170 4060 50 66 109 125 0 488 297 191 2.175 463 167 .46 2.165 1.121 1.114
4 677 1285 97 269 580 1016 757 1333 115 282 660 1064 0 0 464 853 86 144 69 75 66 68 1596 1724 .571 1.752 1.612 2.099 1.884 2.294 208 618 1.933 .9 160 3350 4050 49 65 127 143 0 1382 289 1092 1.884 1433 1144 .531 1.733 .913 .794
5 292 627 90 226 202 401 298 611 103 255 208 385 0 0 152 370 63 141 75 75 67 59 603 593 .504 1.985 1.851 2.184 2.04 2.816 208 665 3.427 .58 160 3540 4050 49 65 146 162 0 674 243 431 2.135 657 414 .468 1.99 1.094 .993
6 308 400 91 223 217 177 303 393 108 250 212 170 0 0 142 200 80 144 86 54 73 23 394 382 1.226 .816 .802 .913 .957 2.554 156 555 1.914 .41 140 3730 4050 50 64 166 180 0 430 240 190 .877 423 183 1.14 .862 -.189 -.214
7 3191 6276 94 230 3097 6046 3282 6302 106 257 3188 6072 0 0 2213 4254 75 145 83 89 81 86 9143 9260 .512 1.952 1.905 2.288 2.059 2.324 208 788 2.023 .93 170 3930 4050 48 65 184 201 0 6748 247 6501 2.099 6776 6529 .476 2.048 1.07 1.034
8 1567 2637 95 239 1472 2398 1643 2799 106 263 1548 2560 0 0 1229 1991 62 148 77 81 72 75 3870 4108 .614 1.629 1.654 1.936 1.722 2.669 208 735 1.705 .9 170 4120 4050 48 65 203 220 0 2835 257 2578 1.752 3010 2753 .571 1.778 .809 .83
9 796 1428 93 226 703 1202 832 1440 106 253 739 1214 0 0 567 1028 79 149 71 74 69 71 1905 1953 .585 1.71 1.643 1.853 1.752 2.457 208 592 1.886 .88 160 4300 4060 50 66 222 238 0 1535 243 1292 1.839 1548 1305 .544 1.766 .879 .821
10 210 389 92 220 118 169 202 358 109 242 110 138 0 0 135 190 89 137 62 50 16 30 287 248 .698 1.432 1.255 1.633 1.817 3.614 208 657 2.427 .36 160 4480 4060 50 66 240 256 0 418 237 182 1.54 385 148 .649 1.349 .623 .432
11 302 818 90 219 212 599 274 848 109 237 184 629 0 0 176 390 88 124 86 84 53 76 811 813 .354 2.825 3.418 2.728 3.048 2.468 156 570 3.875 .56 150 4680 4070 51 66 260 275 0 880 235 644 3.038 912 676 .329 3.676 1.603 1.878
12 160 306 85 213 75 93 128 262 102 232 43 49 0 0 96 195 76 126 39 31 16 18 168 92 .806 1.24 1.14 2.284 2.388 4.85 156 546 3.864 .34 140 4860 4060 51 65 279 293 0 329 229 100 1.333 282 53 .75 1.225 .415 .293
13 1100 687 86 205 1014 482 1227 631 99 228 1141 426 0 0 751 461 58 130 80 71 75 61 1496 1567 2.104 .475 .373 .601 .534 3.481 208 722 .472 .74 170 5060 4060 49 66 297 314 0 739 220 518 .511 678 458 1.956 .401 -.968 -1.317
14 246 341 87 208 159 133 255 312 98 236 168 104 0 0 144 177 52 145 71 42 65 18 292 272 1.195 .836 .619 1.059 1.08 3.54 208 634 3.538 .49 160 5240 4060 50 66 316 332 0 367 224 143 .899 335 112 1.112 .666 -.153 -.587
15 261 551 90 233 171 318 258 517 104 264 168 284 0 0 175 303 94 165 67 62 42 44 489 452 .538 1.86 1.69 1.854 2.198 2.716 208 695 2.876 .55 160 5430 4060 50 66 335 351 0 592 251 342 2 556 305 .5 1.818 1 .862
16 1773 5213 99 249 1674 4964 1814 5259 115 274 1715 5010 0 0 1332 4315 103 155 78 81 75 76 6638 6725 .337 2.965 2.921 2.803 3.047 2.151 208 785 3.285 .93 170 5630 4060 49 66 354 371 0 5605 268 5338 3.189 5655 5387 .314 3.141 1.673 1.651
17 272 534 98 234 174 300 276 511 113 258 178 277 0 0 137 269 77 140 78 67 58 50 474 455 .58 1.724 1.556 1.895 2.01 2.913 156 662 2.991 .53 150 5810 4060 50 65 373 388 0 574 252 323 1.854 549 298 .539 1.673 .891 .743
18 194 313 91 213 103 100 147 266 106 237 56 53 0 0 137 209 84 131 42 30 22 13 203 109 1.03 .971 .946 1.569 1.527 5.281 120 566 2.637 .36 130 6010 4060 51 64 394 407 0 337 229 108 1.044 286 57 .958 1.018 .062 .025
19 256 346 90 224 166 122 243 331 105 243 153 107 0 0 160 185 77 129 73 44 49 20 288 260 1.361 .735 .699 1.138 1.157 3.668 208 707 1.898 .28 160 6200 4070 51 67 412 428 0 372 241 131 .79 356 115 1.265 .752 -.34 -.411
20 174 276 89 206 85 70 158 257 105 229 69 51 0 0 83 157 78 129 43 29 18 9 155 120 1.214 .824 .739 1.455 1.246 4.076 156 550 8.902 .17 150 6390 4070 51 66 431 446 0 297 222 75 .886 276 55 1.129 .795 -.175 -.331

Total number of rows: 7680

Table truncated, full table size 1685 Kbytes.




Supplementary data files not provided
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