NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM90620 Query DataSets for GSM90620
Status Public on Jan 05, 2006
Title Skin 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 skin cell line RNA labeled with amino allyl
Organism Homo sapiens
Characteristics 20 ug total skin 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/2002-01/24769.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
1 177 145 85 46 92 99 181 138 85 49 96 92 0 0 37 45 19 17 98 98 96 92 191 188 .929 1.076 .958 1.006 1.028 2.028 52 280 1.073 .67 80 1840 8870 58 66 109 117 0 101 32 69 .753 97 64 1.329 .67 -.41 -.577
2 210 161 87 47 123 114 210 153 88 49 123 106 0 0 59 61 22 19 96 98 94 96 237 229 1.079 .927 .862 .914 .925 1.984 52 325 .894 .77 90 1990 8870 57 66 123 132 0 113 33 80 .648 107 74 1.543 .603 -.626 -.731
3 329 586 88 47 241 539 340 602 90 51 252 555 0 0 73 170 25 26 100 100 98 100 780 807 .447 2.237 2.202 2.256 2.215 1.448 52 325 2.284 .9 90 2130 8860 56 65 137 146 0 410 33 377 1.564 421 388 .639 1.54 .645 .623
4 274 267 90 44 184 223 254 267 92 49 164 223 0 0 94 114 24 20 96 100 92 96 407 387 .825 1.212 1.36 1.23 1.235 1.886 52 280 1.255 .8 80 2280 8870 58 66 153 161 0 187 31 156 .848 187 156 1.18 .951 -.239 -.073
5 181 120 84 44 97 76 180 119 87 47 96 75 0 0 41 43 21 15 93 96 90 87 173 171 1.276 .784 .781 .823 .72 2.425 32 214 .698 .56 70 2420 8860 57 64 167 174 0 84 31 53 .548 83 52 1.825 .546 -.868 -.872
6 183 168 82 41 101 127 184 164 84 42 102 123 0 0 46 55 21 13 100 100 87 96 228 225 .795 1.257 1.206 1.251 1.249 2.107 32 170 1.168 .59 60 2570 8870 59 65 183 189 0 117 29 89 .879 115 86 1.137 .843 -.186 -.246
7 207 151 85 44 122 107 195 144 88 46 110 100 0 0 66 54 21 15 98 100 92 98 229 210 1.14 .877 .909 .865 .836 2.091 52 254 .758 .6 80 2720 8870 58 66 197 205 0 106 31 75 .613 101 70 1.63 .636 -.705 -.654
8 2165 3637 85 45 2080 3592 2297 3552 86 48 2212 3507 0 0 879 1370 20 17 98 100 98 100 5672 5719 .579 1.727 1.585 1.86 1.79 1.959 80 389 1.77 .91 100 2860 8870 57 67 210 220 0 2543 31 2512 1.208 2484 2452 .828 1.109 .272 .149
9 219 196 79 44 140 152 211 183 81 45 132 139 0 0 84 84 22 16 96 100 92 98 292 271 .921 1.086 1.053 1.119 1.099 2.286 52 278 1.055 .82 80 3010 8870 58 66 226 234 0 137 31 106 .759 128 97 1.317 .736 -.397 -.441
10 184 149 82 42 102 107 179 140 83 46 97 98 0 0 54 66 19 18 96 90 90 84 209 195 .953 1.049 1.01 .913 1.038 2.069 32 153 1.119 .65 60 3160 8870 59 65 242 248 0 104 29 75 .734 98 69 1.363 .707 -.447 -.501
11 461 525 84 43 377 482 431 434 87 47 347 391 0 0 219 292 47 34 93 100 90 100 859 738 .782 1.279 1.127 1.309 1.274 1.825 80 370 1.307 .9 100 3300 8870 57 67 254 264 0 367 30 337 .894 303 273 1.118 .788 -.162 -.344
12 224 233 82 43 142 190 217 235 86 49 135 192 0 0 68 80 55 42 90 100 65 90 332 327 .747 1.338 1.422 1.381 1.487 1.852 52 256 .334 .47 80 3450 8870 58 66 270 278 0 163 30 133 .936 164 134 1.069 .995 -.096 -.008
13 227 230 82 43 145 187 211 212 82 47 129 169 0 0 82 104 20 20 98 96 94 92 332 298 .775 1.29 1.31 1.24 1.365 2.133 52 328 1.306 .79 90 3600 8870 57 66 284 293 0 161 30 131 .902 148 118 1.109 .916 -.149 -.126
14 147 81 81 45 66 36 141 82 83 46 60 37 0 0 38 26 19 14 90 68 68 65 102 97 1.833 .545 .617 .528 .548 2.483 32 158 .451 .56 60 3740 8870 59 65 300 306 0 57 31 25 .381 57 26 2.622 .431 -1.39 -1.213
15 784 1416 81 44 703 1372 768 1441 82 46 687 1397 0 0 288 633 21 14 98 100 98 100 2075 2084 .512 1.952 2.033 1.899 2.084 1.756 80 389 2.092 .93 100 3890 8870 57 67 313 323 0 990 31 959 1.365 1008 977 .733 1.422 .449 .508
16 248 341 78 43 170 298 252 344 80 45 174 301 0 0 85 95 21 14 92 100 91 100 468 475 .57 1.753 1.73 1.98 1.798 2.055 80 350 1.696 .87 100 4030 8870 57 67 327 337 0 238 30 208 1.226 241 210 .816 1.21 .294 .275
17 188 181 77 43 111 138 188 176 79 48 111 133 0 0 57 72 25 46 92 94 84 73 249 244 .804 1.243 1.198 1.204 1.112 2.311 52 320 1.582 .66 90 4170 8870 57 66 341 350 0 127 30 97 .869 123 93 1.15 .838 -.202 -.255
18 179 134 78 45 101 89 179 127 81 50 101 82 0 0 43 53 29 48 100 75 80 42 190 183 1.135 .881 .812 .757 .958 2.607 52 276 .885 .66 80 4330 8880 59 67 358 366 0 94 31 62 .616 89 57 1.623 .568 -.698 -.817
19 348 402 84 46 264 356 344 426 89 50 260 380 0 0 107 135 37 25 100 100 100 100 620 640 .742 1.348 1.462 1.359 1.48 1.581 52 338 1.38 .84 90 4470 8860 56 65 371 380 0 281 32 249 .943 298 266 1.06 1.022 -.085 .031
20 216 209 83 46 133 163 196 190 85 49 113 144 0 0 81 86 22 20 100 100 96 100 296 257 .816 1.226 1.274 1.26 1.345 1.81 32 200 1.161 .75 70 4620 8880 59 66 387 394 0 146 32 114 .857 133 101 1.167 .891 -.223 -.166

Total number of rows: 43008

Table truncated, full table size 9303 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap