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Sample GSM90641 Query DataSets for GSM90641
Status Public on Jan 05, 2006
Title fibroblast 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 fibroblast cell line
Organism Mus musculus
Characteristics fibroblast cell line
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tissue, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20143.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 2684 3175 74 216 2610 2959 3311 3710 88 249 3237 3494 0 0 1900 2423 63 198 77 76 75 70 5569 6731 .882 1.134 1.079 1.283 1.069 2.564 208 934 1.227 .89 160 2770 4130 57 73 69 85 0 3649 248 3401 1.303 4264 4016 .767 1.241 .382 .311
2 184 337 73 203 111 134 195 325 90 295 122 122 0 0 94 169 80 1017 60 0 31 0 245 244 .828 1.207 1 1.621 1.541 3.987 208 648 4.138 .41 160 2950 4130 57 73 87 103 0 387 233 154 1.388 374 140 .721 1.149 .473 .201
3 306 1158 71 203 235 955 169 305 89 289 98 102 0 0 1419 5460 89 1053 57 5 20 4 1190 200 .246 4.064 1.041 1.974 2.074 3.293 208 592 4.51 .84 160 3150 4140 58 74 107 123 0 1331 233 1098 4.671 351 117 .214 1.196 2.224 .259
4 1387 994 70 201 1317 793 1491 989 79 224 1421 788 0 0 1133 729 50 136 70 71 69 64 2110 2209 1.661 .602 .555 .926 .678 3.631 208 618 .608 .92 160 3330 4130 57 73 125 141 0 1143 231 911 .692 1137 906 1.445 .637 -.531 -.65
5 379 486 68 195 311 291 413 463 76 220 345 268 0 0 225 274 45 134 76 66 73 50 602 613 1.069 .936 .777 1.045 .917 2.766 208 665 1.298 .63 160 3520 4130 57 73 144 160 0 559 224 334 1.076 532 308 .93 .893 .105 -.163
6 356 343 65 188 291 155 342 268 75 212 277 80 0 0 270 278 54 135 85 35 81 18 446 357 1.877 .533 .289 .554 .496 3.628 156 555 .993 .39 140 3710 4130 58 72 164 178 0 394 216 178 .612 308 92 1.633 .332 -.708 -1.591
7 3599 6633 66 200 3533 6433 4080 7306 75 218 4014 7106 0 0 2997 5245 49 132 77 82 73 77 9966 11120 .549 1.821 1.77 2.334 1.879 2.502 208 788 1.798 .95 170 3910 4130 56 73 182 199 0 7624 230 7394 2.093 8398 8168 .478 2.035 1.066 1.025
8 2151 2822 67 197 2084 2625 2503 3092 79 215 2436 2895 0 0 1488 1960 78 128 76 83 75 79 4709 5331 .794 1.26 1.188 1.61 1.266 2.34 208 735 1.315 .92 170 4100 4130 56 73 201 218 0 3244 226 3017 1.448 3554 3328 .691 1.366 .534 .45
9 1101 1387 68 200 1033 1187 1192 1539 84 219 1124 1339 0 0 815 935 105 127 72 77 71 72 2220 2463 .87 1.149 1.191 1.583 1.245 2.904 208 592 1.173 .91 160 4280 4140 58 74 220 236 0 1594 230 1364 1.321 1769 1539 .757 1.369 .401 .453
10 150 272 68 199 82 73 143 254 79 216 75 55 0 0 82 150 74 117 50 34 13 12 155 130 1.123 .89 .733 1.764 1.903 4.167 208 657 6.396 .22 160 4460 4140 58 74 238 254 0 313 229 84 1.023 292 63 .977 .843 .033 -.247
11 351 510 66 192 285 318 346 487 74 216 280 295 0 0 241 248 40 129 89 78 84 56 603 575 .896 1.116 1.054 1.199 1.318 2.844 156 570 1.259 .63 150 4660 4150 59 74 258 273 0 586 221 366 1.283 560 339 .78 1.211 .359 .276
12 168 285 65 189 103 96 120 251 74 214 55 62 0 0 120 194 44 140 53 32 44 12 199 117 1.073 .932 1.127 1.577 1.611 4.863 156 546 3.747 .35 140 4840 4140 59 73 277 291 0 328 217 110 1.071 289 71 .933 1.296 .099 .374
13 1776 1432 71 212 1705 1220 2143 1528 86 273 2072 1316 0 0 1392 999 79 421 70 66 68 61 2925 3388 1.398 .716 .635 1.086 .771 3.328 208 722 .757 .81 170 5040 4140 57 74 295 312 0 1646 244 1402 .822 1756 1513 1.216 .73 -.282 -.454
14 247 312 71 223 176 89 260 277 88 296 189 54 0 0 158 209 81 460 68 3 56 0 265 243 1.978 .506 .286 .996 .799 4.186 208 639 19.145 .14 160 5220 4140 58 74 314 330 0 359 256 102 .581 318 62 1.72 .328 -.783 -1.606
15 349 462 66 199 283 263 372 411 75 241 306 212 0 0 206 275 47 210 78 50 73 22 546 518 1.076 .929 .693 1.023 .951 3.394 208 707 1.52 .52 160 5410 4140 58 74 333 349 0 531 229 302 1.068 472 244 .936 .796 .095 -.329
16 2745 1446 65 192 2680 1254 3048 1564 77 223 2983 1372 0 0 2310 1105 60 158 72 71 70 66 3934 4355 2.137 .468 .46 .776 .506 3.453 208 790 .451 .92 170 5610 4140 57 74 352 369 0 1662 221 1441 .538 1798 1577 1.859 .529 -.895 -.92
17 284 361 66 187 218 174 307 319 80 208 241 132 0 0 133 260 62 126 82 51 74 26 392 373 1.253 .798 .548 .797 .825 3.128 156 662 2.284 .41 150 5790 4140 58 73 371 386 0 415 215 200 .917 367 152 1.09 .63 -.124 -.668
18 226 295 67 181 159 114 163 256 82 201 96 75 0 0 169 191 69 119 53 40 42 26 273 171 1.395 .717 .781 1.417 1.085 3.97 120 566 1.639 .49 130 5990 4140 59 72 392 405 0 339 208 131 .824 294 86 1.213 .898 -.279 -.155
19 218 299 66 180 152 119 231 269 77 205 165 89 0 0 121 174 58 126 71 42 62 20 271 254 1.277 .783 .539 1.151 1.068 3.861 208 707 2.483 .41 160 6180 4150 59 75 410 426 0 344 207 137 .9 309 102 1.111 .62 -.152 -.69
20 182 283 65 181 117 102 174 253 73 202 109 72 0 0 116 164 37 117 71 38 62 17 219 181 1.147 .872 .661 1.143 1.211 3.611 156 550 3.49 .32 150 6370 4150 59 74 429 444 0 325 208 117 1.002 291 83 .998 .759 .003 -.397

Total number of rows: 7680

Table truncated, full table size 1684 Kbytes.




Supplementary data files not provided
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