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Sample GSM63330 Query DataSets for GSM63330
Status Public on Jul 09, 2005
Title Human Malaria __raw_ 9
Sample type RNA
 
Channel 1
Source name reference
Organism Homo sapiens
Characteristics Stratagene, amplified with Ambion method
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name clinical sample
Organism Homo sapiens
Characteristics 11_Malaria; PAXgene sample
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37525.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 Jul 08, 2005
Last update date Nov 16, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
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 GPL2614
Series (1)
GSE2900 Host Response Malaria

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 same as UNF_VALUE but with flagged values removed
UNF_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 UNF_VALUE
1 1985 2152 141 205 1844 1947 1687 1886 145 214 1546 1681 0 0 901 1029 31 87 100 100 100 100 3791 3227 .947 1.056 1.087 1.017 1.002 1.338 80 380 1.089 .95 100 1390 7050 76 86 42 52 0 2060 196 1864 1.011 1806 1609 .989 1.041 .016 .058 .058
2 2078 3412 146 209 1932 3203 1762 3317 148 215 1616 3108 0 0 847 1340 31 78 100 100 100 100 5135 4724 .603 1.658 1.923 1.664 1.667 1.286 80 458 1.69 .96 110 1550 7050 75 86 57 68 0 3267 200 3066 1.587 3176 2975 .63 1.841 .666 .881 .881
3 1902 1571 150 207 1752 1364 1911 1572 152 217 1761 1365 0 0 730 619 36 80 100 98 100 97 3116 3126 1.284 .779 .775 .766 .762 1.37 80 426 .789 .95 110 1710 7060 76 87 73 84 0 1504 198 1306 .745 1505 1307 1.342 .742 -.424 -.43 -.43
4 1772 2119 146 206 1626 1913 1643 1868 150 217 1497 1662 0 0 732 1018 36 78 100 100 100 100 3539 3159 .85 1.177 1.11 1.128 1.174 1.384 80 419 1.251 .95 110 1850 7020 72 83 87 98 0 2029 197 1831 1.126 1788 1591 .888 1.063 .172 .088 .088
5 1027 853 148 212 879 641 1082 876 154 220 934 664 0 0 458 356 46 81 96 93 93 88 1520 1598 1.371 .729 .711 .738 .729 2.277 80 364 .734 .9 100 2000 7030 74 84 103 113 0 817 203 614 .698 839 636 1.432 .681 -.518 -.555 -.555
6 1601 4955 154 231 1447 4724 1546 4699 164 249 1392 4468 0 0 532 1994 70 193 100 100 100 100 6171 5860 .306 3.265 3.21 3.196 3.228 1.369 80 459 3.599 .94 110 2160 7020 72 83 118 129 0 4744 221 4523 3.125 4499 4278 .32 3.073 1.644 1.62 1.62
7 3534 5197 149 229 3385 4968 3294 4942 156 245 3145 4713 0 0 1432 2216 63 180 100 100 100 100 8353 7858 .681 1.468 1.499 1.459 1.463 1.279 80 440 1.489 .97 110 2340 7040 74 85 136 147 0 4975 219 4756 1.405 4731 4512 .712 1.435 .491 .521 .521
8 1078 1231 147 217 931 1014 1082 1138 150 224 935 921 0 0 443 542 41 85 100 100 100 100 1945 1856 .918 1.089 .985 1.058 1.084 1.39 80 375 1.133 .95 100 2500 7050 76 86 153 163 0 1179 208 971 1.043 1089 882 .959 .943 .06 -.085 -.085
9 2596 4983 145 219 2451 4764 2543 5110 160 242 2398 4891 0 0 856 1709 96 144 100 100 100 100 7215 7289 .514 1.944 2.04 1.94 1.983 1.32 52 301 1.969 .95 90 2650 7050 76 85 168 177 0 4771 210 4561 1.861 4892 4682 .537 1.953 .896 .965 .965
10 4110 6902 144 215 3966 6687 3805 6293 165 255 3661 6078 0 0 2462 4115 120 244 98 97 98 96 10653 9739 .593 1.686 1.66 1.638 1.632 1.667 80 397 1.701 .98 110 2810 7060 76 87 183 194 0 6608 206 6402 1.614 6025 5819 .62 1.589 .691 .668 .668
11 3416 5537 149 215 3267 5322 3226 5174 157 228 3077 4959 0 0 1339 2342 53 97 100 100 100 100 8589 8036 .614 1.629 1.612 1.615 1.572 1.267 80 353 1.688 .96 100 2970 7040 75 85 200 210 0 5301 206 5095 1.56 4953 4748 .641 1.543 .641 .626 .626
12 2075 3038 150 216 1925 2822 1888 2570 155 222 1738 2354 0 0 1249 1892 37 75 100 100 100 100 4747 4092 .682 1.466 1.354 1.483 1.452 1.435 80 363 1.505 .96 100 3130 7050 76 86 216 226 0 2908 207 2702 1.403 2460 2254 .713 1.297 .489 .375 .375
13 2043 3354 154 219 1889 3135 1669 2784 156 222 1515 2565 0 0 1017 1798 36 74 100 100 100 100 5024 4080 .603 1.66 1.693 1.62 1.633 1.296 80 398 1.716 .97 110 3280 7040 74 85 230 241 0 3211 210 3001 1.589 2665 2456 .629 1.621 .668 .697 .697
14 7666 8583 151 216 7515 8367 6356 7403 150 223 6205 7187 0 0 4769 4881 33 77 100 100 99 100 15882 13392 .898 1.113 1.158 1.244 1.111 1.775 120 462 1.086 .95 120 3440 7040 74 86 246 258 0 8217 207 8010 1.066 7087 6881 .938 1.109 .092 .149 .149
15 4365 7309 145 219 4220 7090 3596 6575 146 223 3451 6356 0 0 2441 4182 30 83 100 100 100 100 11310 9807 .595 1.68 1.842 1.659 1.745 1.333 80 361 1.721 .96 110 3600 7050 75 86 262 273 0 6997 210 6788 1.608 6295 6085 .622 1.763 .686 .818 .818
16 4262 23048 141 219 4121 22829 4054 22098 144 233 3913 21879 0 0 1413 7242 32 99 100 100 100 100 26950 25792 .181 5.54 5.591 5.59 5.611 1.245 80 391 5.671 .97 110 3750 7040 74 85 277 288 0 22065 210 21856 5.303 21156 20946 .189 5.353 2.407 2.42 2.42
17 3637 2880 142 222 3495 2658 3367 2586 144 234 3225 2364 0 0 1682 1329 31 94 100 100 100 100 6153 5589 1.315 .761 .733 .75 .775 1.278 80 377 .764 .97 110 3910 7050 75 86 293 304 0 2757 213 2545 .728 2476 2263 1.373 .702 -.458 -.511 -.511
18 2074 4013 141 219 1933 3794 1938 3759 142 228 1797 3540 0 0 786 1653 27 80 100 100 100 100 5727 5337 .509 1.963 1.97 1.932 1.92 1.25 80 338 2.023 .97 100 4070 7050 76 86 310 320 0 3842 210 3632 1.879 3599 3389 .532 1.886 .91 .915 .915
19 529 465 143 218 386 247 177 306 146 220 34 88 0 0 642 409 29 78 53 52 42 36 633 122 1.563 .64 2.588 1.205 .871 3.399 80 356 .623 .88 100 4230 7040 75 85 326 336 -50 445 209 236 .613 293 84 1.632 2.478 -.707 1.309
20 1509 1411 146 220 1363 1191 1373 1433 146 221 1227 1213 0 0 641 602 30 80 98 98 98 98 2554 2440 1.144 .874 .989 .83 .831 1.426 52 247 .886 .94 80 4380 7050 77 85 342 350 0 1351 211 1140 .837 1372 1161 1.195 .946 -.257 -.079 -.079

Total number of rows: 37632

Table truncated, full table size 9011 Kbytes.




Supplementary data files not provided
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