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Sample GSM90640 Query DataSets for GSM90640
Status Public on Jan 05, 2006
Title kidney 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 kidney cell line
Organism Mus musculus
Characteristics kidney cell line
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tissue, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20142.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 5618 2886 79 183 5539 2703 7117 3255 90 201 7038 3072 0 0 4303 2293 55 114 78 77 74 73 8242 10110 2.049 .488 .436 .673 .491 2.996 208 934 .475 .89 160 2760 4110 55 71 68 84 0 2975 189 2787 .503 3356 3167 1.988 .45 -.991 -1.152
2 278 280 78 172 200 108 267 248 89 186 189 76 0 0 174 163 58 108 73 45 68 22 308 265 1.852 .54 .402 .777 .829 3.789 208 648 .835 .41 160 2940 4110 55 71 86 102 0 289 177 111 .557 256 78 1.796 .415 -.845 -1.27
3 193 279 81 185 112 94 159 238 94 205 78 53 0 0 205 260 58 118 60 30 32 15 206 131 1.191 .839 .679 1.459 1.584 3.484 208 592 1.608 .63 160 3140 4120 56 72 106 122 0 288 191 97 .865 245 55 1.156 .701 -.209 -.514
4 1068 980 82 189 986 791 1090 893 95 216 1008 704 0 0 760 736 60 142 79 78 75 69 1777 1712 1.247 .802 .698 .907 .774 2.615 208 618 .879 .87 160 3320 4110 55 71 124 140 0 1010 195 815 .827 921 726 1.209 .72 -.274 -.474
5 255 370 78 178 177 192 230 343 90 198 152 165 0 0 166 215 57 128 73 56 60 33 369 317 .922 1.085 1.086 1.187 1.254 3.417 208 665 1.615 .59 160 3510 4110 55 71 143 159 0 381 184 198 1.118 354 170 .894 1.119 .161 .162
6 288 241 79 174 209 67 275 213 90 197 196 39 0 0 142 136 52 138 89 21 80 7 276 235 3.119 .321 .199 .476 .452 3.502 156 555 .574 .2 140 3700 4110 56 70 163 177 0 248 179 69 .33 220 40 3.026 .205 -1.597 -2.285
7 5726 8949 80 180 5646 8769 6853 10471 92 213 6773 10291 0 0 4075 6110 78 209 85 87 82 82 14415 17064 .644 1.553 1.519 1.866 1.587 2.384 208 808 1.563 .95 170 3900 4110 54 71 181 198 0 9226 186 9040 1.601 10795 10609 .625 1.566 .679 .647
8 1696 1230 80 182 1616 1048 1986 1241 95 209 1906 1059 0 0 1176 864 70 148 77 77 76 74 2664 2965 1.542 .649 .556 .837 .678 3.019 208 778 .657 .87 170 4090 4110 54 71 200 217 0 1268 188 1080 .669 1279 1092 1.496 .573 -.581 -.804
9 1182 1334 78 181 1104 1153 1403 1413 93 203 1325 1232 0 0 854 971 63 135 74 75 72 71 2257 2557 .958 1.044 .93 1.306 1.049 2.463 208 614 1.107 .9 160 4270 4120 56 72 219 235 0 1375 187 1189 1.077 1457 1270 .929 .959 .107 -.061
10 173 225 77 175 96 50 165 214 92 200 88 39 0 0 112 112 71 121 58 23 17 6 146 127 1.92 .521 .443 1.118 1.173 4.278 208 657 11.752 .04 160 4450 4120 56 72 237 253 0 232 180 52 .537 221 40 1.862 .457 -.897 -1.13
11 299 273 75 181 224 92 283 243 87 200 208 62 0 0 179 161 53 118 85 33 81 15 316 270 2.435 .411 .298 .624 .627 4.003 156 608 .742 .26 150 4650 4130 57 72 257 272 0 281 187 95 .423 251 64 2.362 .307 -1.24 -1.702
12 188 260 76 183 112 77 174 233 87 201 98 50 0 0 99 172 45 110 71 35 54 20 189 148 1.455 .688 .51 1.557 1.528 3.679 120 460 4.731 .21 120 4840 4120 58 70 278 290 0 268 189 79 .709 240 52 1.411 .526 -.497 -.927
13 946 599 79 203 867 396 1102 574 90 215 1023 371 0 0 631 396 52 114 78 73 75 64 1263 1394 2.189 .457 .363 .599 .489 3.183 208 740 .477 .75 170 5030 4120 55 72 294 311 0 618 209 408 .471 592 382 2.124 .374 -1.087 -1.419
14 211 232 79 196 132 36 216 212 94 211 137 16 0 0 117 149 61 119 68 19 54 6 168 153 3.667 .273 .117 .818 .811 4.339 208 639 -1 -1 160 5210 4120 56 72 313 329 0 239 202 37 .281 219 16 3.557 .12 -1.831 -3.054
15 266 275 82 186 184 89 240 263 96 207 158 77 0 0 181 131 67 121 75 37 59 12 273 235 2.067 .484 .487 .859 .947 4.043 208 724 .643 .22 160 5400 4120 56 72 332 348 0 284 192 92 .499 271 79 2.005 .502 -1.004 -.993
16 5897 646 84 187 5813 459 7010 653 96 207 6926 466 0 0 3773 367 64 115 85 78 83 70 6272 7392 12.664 .079 .067 .092 .078 2.697 208 789 .071 .8 170 5600 4120 55 72 351 368 0 666 193 473 .081 673 480 12.285 .069 -3.619 -3.85
17 284 245 83 181 201 64 299 234 91 202 216 53 0 0 113 116 59 112 83 33 76 8 265 269 3.141 .318 .245 .54 .518 3.143 156 642 .84 .32 150 5780 4120 56 71 370 385 0 253 187 66 .328 241 55 3.046 .253 -1.607 -1.983
18 209 300 78 170 131 130 135 227 86 188 57 57 0 0 197 247 52 107 54 40 35 22 261 114 1.008 .992 1 1.464 1.41 4.856 120 610 2.067 .42 130 5980 4120 57 70 391 404 0 309 175 134 1.023 234 59 .977 1.031 .033 .044
19 220 260 77 171 143 89 203 242 86 185 126 71 0 0 128 137 43 100 80 41 64 22 232 197 1.607 .622 .563 .853 .966 3.259 156 691 1.663 .32 140 6180 4100 55 69 411 425 0 268 176 92 .642 249 73 1.559 .581 -.64 -.784
20 191 251 76 177 115 74 174 225 85 191 98 48 0 0 92 144 45 106 80 33 55 16 189 146 1.554 .643 .49 .985 .974 3.574 120 504 3.242 .33 130 6370 4120 57 70 430 443 0 259 182 76 .663 232 49 1.507 .505 -.592 -.986

Total number of rows: 7680

Table truncated, full table size 1681 Kbytes.




Supplementary data files not provided
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