NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM93280 Query DataSets for GSM93280
Status Public on Jan 21, 2006
Title VU32 24h LAsp
Sample type RNA
 
Channel 1
Source name Stratagene amp
Organism Homo sapiens
Characteristics Stratagene amp
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name VU32 24h LAsp
Organism Homo sapiens
Characteristics VU32 24h LAsp
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: acute lymphoblastic leukemia, untreated
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38902.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Jan 19, 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 GPL3322
Series (2)
GSE4071 Clinical pediatric acute lymphoblastic leukemia samples after in vitro exposure to L-asparaginase
GSE4397 In vitro response to l-asparaginase in acute lymphoblastic leukemia

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 values 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 value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value 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 value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value 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
LOG_RAT2N_MEAN 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
VALUE 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 LOG_RAT2N_MEAN VALUE
1 1251 1070 177 192 1074 878 1235 971 177 200 1058 779 0 0 604 545 29 84 94 96 94 92 1952 1837 1.223 .818 .736 .792 .759 1.514 52 267 .839 .93 80 1960 8470 31 39 84 92 0 1359 244 1115 1.038 1233 989 .963 .935 .054 -.097
2 14879 1838 181 190 14698 1648 14895 1983 182 204 14714 1793 0 0 7270 847 29 88 100 100 100 100 16346 16507 8.919 .112 .122 .111 .108 1.28 52 304 .11 .97 90 2110 8470 30 39 98 107 0 2334 241 2093 .142 2518 2277 7.022 .155 -2.812 -2.692
3 3491 1725 181 200 3310 1525 3314 1667 183 208 3133 1467 0 0 1827 850 30 73 100 100 100 100 4835 4600 2.17 .461 .468 .468 .461 1.37 32 171 .45 .97 60 2250 8460 31 37 114 120 0 2191 254 1937 .585 2117 1863 1.709 .595 -.773 -.75
4 4438 1076 180 205 4258 871 4206 1053 185 205 4026 848 0 0 2382 624 41 71 100 100 100 93 5129 4874 4.889 .205 .211 .195 .192 1.427 32 214 .212 .92 70 2390 8460 30 37 127 134 0 1367 260 1106 .26 1337 1077 3.849 .268 -1.945 -1.902
5 7010 8167 180 196 6830 7971 6907 8739 183 205 6727 8543 0 0 4174 4395 35 79 92 100 92 98 14801 15270 .857 1.167 1.27 1.311 1.193 1.628 52 336 1.128 .99 90 2540 8460 29 38 141 150 0 10372 249 10123 1.482 11099 10850 .675 1.613 .568 .69
6 1266 1166 189 201 1077 965 1251 1114 190 210 1062 913 0 0 674 689 42 81 90 94 88 84 2042 1975 1.116 .896 .86 .833 .866 1.437 52 264 .933 .94 80 2690 8460 30 38 157 165 0 1481 255 1226 1.138 1415 1160 .879 1.092 .186 .127
7 4428 4876 182 206 4246 4670 4278 4891 184 209 4096 4685 0 0 2499 2688 32 88 100 100 100 100 8916 8781 .909 1.1 1.144 1.143 1.079 1.333 52 300 1.093 .98 90 2840 8470 30 39 171 180 0 6193 262 5931 1.397 6212 5950 .716 1.453 .482 .539
8 2944 2435 183 218 2761 2217 2829 2270 185 227 2646 2052 0 0 1612 1408 32 91 100 98 100 96 4978 4698 1.245 .803 .776 .764 .797 1.372 52 288 .813 .97 90 2990 8470 30 39 186 195 0 3093 277 2816 1.02 2883 2606 .981 .985 .028 -.022
9 4199 3967 181 216 4018 3751 4952 4399 184 228 4771 4183 0 0 2024 1891 32 89 96 98 96 98 7769 8954 1.071 .934 .877 .972 .906 1.384 80 358 .933 .98 100 3130 8460 29 39 200 210 0 5038 274 4764 1.186 5587 5313 .843 1.114 .246 .155
10 2953 1882 181 208 2772 1674 2762 1802 185 223 2581 1594 0 0 1653 1058 31 88 94 96 94 94 4446 4175 1.656 .604 .618 .605 .579 1.358 52 276 .606 .97 90 3280 8460 29 38 215 224 0 2390 264 2126 .767 2289 2024 1.304 .784 -.383 -.35
11 12624 4103 180 199 12444 3904 14074 4272 181 208 13894 4073 0 0 6246 2072 31 88 98 98 98 98 16348 17967 3.188 .314 .293 .339 .312 1.535 80 356 .312 .98 100 3420 8460 29 39 229 239 0 5211 253 4958 .398 5426 5173 2.51 .372 -1.328 -1.425
12 26621 23625 170 189 26451 23436 26932 22549 174 205 26762 22360 0 0 12652 10455 33 88 100 100 100 100 49887 49122 1.129 .886 .836 .959 .869 1.368 80 403 .869 .99 110 3570 8460 28 39 243 254 0 30005 240 29764 1.125 28638 28398 .889 1.061 .17 .086
13 13484 15551 170 191 13314 15360 13214 14864 173 202 13044 14673 0 0 8081 8612 31 81 100 100 100 100 28674 27717 .867 1.154 1.125 1.271 1.139 1.492 80 325 1.124 .99 100 3720 8460 29 39 259 269 0 19750 243 19508 1.465 18878 18635 .682 1.429 .551 .515
14 3135 2423 173 189 2962 2234 3303 2429 176 201 3130 2240 0 0 1047 812 38 82 100 100 100 100 5196 5370 1.326 .754 .716 .759 .769 1.302 120 406 .748 .97 120 3860 8460 28 40 272 284 0 3077 240 2837 .958 3085 2845 1.044 .909 -.062 -.138
15 6044 5810 182 191 5862 5619 5429 5549 185 205 5247 5358 0 0 3105 3070 40 91 100 100 100 100 11481 10605 1.043 .959 1.021 .961 .961 1.204 120 356 .968 .99 120 4010 8460 28 40 287 299 0 7379 243 7136 1.217 7047 6805 .821 1.297 .284 .375
16 17351 18965 189 204 17162 18761 15997 17700 192 214 15808 17496 0 0 5976 6805 36 94 100 100 100 100 35923 33304 .915 1.093 1.107 1.103 1.061 1.225 120 431 1.099 .99 130 4150 8460 27 40 300 313 0 24086 259 23827 1.388 22480 22221 .72 1.406 .473 .491
17 19298 24572 189 207 19109 24365 18779 23311 192 219 18590 23104 0 0 8691 11361 36 87 100 100 100 100 43474 41694 .784 1.275 1.243 1.283 1.223 1.258 120 425 1.285 .98 120 4300 8460 28 40 316 328 0 31207 263 30944 1.619 29606 29343 .618 1.578 .695 .658
18 526 334 185 213 341 121 252 247 189 223 67 34 0 0 586 226 33 85 59 40 50 25 462 101 2.818 .355 .507 .725 .5 4.183 52 227 .365 .82 80 4440 8450 29 37 332 340 -50 424 271 154 .451 314 43 2.219 .644 -1.15 -.634
19 16857 25823 193 212 16664 25611 18760 27509 194 221 18567 27297 0 0 7986 12110 33 85 100 100 100 100 42275 45864 .651 1.537 1.47 1.702 1.516 1.576 80 338 1.532 .99 100 4600 8460 29 39 347 357 0 32796 269 32527 1.952 34937 34668 .512 1.867 .965 .901
20 19381 31483 187 219 19194 31264 18971 31490 191 224 18784 31271 0 1 10097 16015 54 90 100 100 100 100 50458 50055 .614 1.629 1.665 1.699 1.58 1.319 120 422 1.624 .99 120 4740 8460 28 40 360 372 0 39984 278 39706 2.069 39993 39715 .483 2.114 1.049 1.08

Total number of rows: 43104

Table truncated, full table size 10046 Kbytes.




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