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Sample GSM333322 Query DataSets for GSM333322
Status Public on Oct 21, 2008
Title B65 Epo-HBP4
Sample type RNA
 
Channel 1
Source Name aRNA by SH on 3/27/03 from cell lines
Organism(s) Homo sapiens
Characteristics aRNA by SH on 3/27/03 from cell lines
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source Name B65 Epo-HBP4
Organism(s) Homo sapiens
Characteristics B65 Epo-HBP4
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.3; Parameter Image Origin = 1280, 9600; Software: type: feature extraction; Performer: Minnie,,Sarwal
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-05-29; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 640; Parameter Laser on time = 100199; Parameter Laser Power = 1.44; Parameter Scan Time = 09:55:21; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.24; Performer: Minnie,,Sarwal
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-05-29; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 720; Parameter Scan Power = 100; Parameter Laser on time = 465308; Parameter Laser Power = 1.94; Parameter Scan Time = 09:55:21; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.24; Performer: Minnie,,Sarwal
Description Simple annotation: Tissue Rejection, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41765.gif
Disease State: B65
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 Oct 14, 2008
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 GPL7486
Series (1)
GSE13198 Erythropoietin use in kidney transplants

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 8972 13130 129 317 8843 12813 1108 4610 137 385 979 4293 1 5 15526 16945 68 365 100 100 100 96 21656 5272 .69 1.449 4.385 2.381 2.369 1.918 80 356 1.259 .92 100 1920 10320 67 77 59 69 -100 11595 280 11315 1.28 4071 3791 .782 3.872 .356 1.953
2 9581 14795 124 285 9457 14510 1176 3552 129 334 1052 3267 2 5 17381 20615 40 241 100 99 98 97 23967 4319 .652 1.534 3.106 2.474 2.47 1.84 120 398 1.366 .91 120 2070 10310 65 77 73 85 -100 13065 252 12814 1.355 3137 2885 .738 2.742 .438 1.455
3 1263 3761 114 223 1149 3538 1244 3824 125 255 1130 3601 0 0 443 1322 64 190 100 100 99 100 4687 4731 .325 3.079 3.187 3.039 3.176 1.405 120 413 3.241 .94 120 2230 10310 65 77 89 101 0 3321 197 3124 2.719 3377 3180 .368 2.814 1.443 1.493
4 740 1206 114 197 626 1009 749 1197 123 224 635 1000 0 0 210 368 63 133 100 100 100 99 1635 1635 .62 1.612 1.575 1.601 1.551 1.371 120 394 1.794 .92 120 2390 10310 65 77 105 117 0 1065 174 891 1.423 1057 883 .703 1.391 .509 .476
5 511 849 113 174 398 675 528 796 115 195 415 622 0 0 148 364 26 99 98 99 97 95 1073 1037 .59 1.696 1.499 1.618 1.556 1.703 120 357 2.249 .81 120 2540 10310 65 77 120 132 0 750 154 596 1.498 703 549 .668 1.324 .583 .404
6 665 1888 113 179 552 1709 646 1816 115 194 533 1637 0 0 234 497 26 87 99 100 99 99 2261 2170 .323 3.096 3.071 3.213 3.123 1.374 120 360 3.441 .88 120 2700 10310 65 77 136 148 0 1667 158 1509 2.734 1604 1446 .366 2.712 1.451 1.439
7 750 1404 119 176 631 1228 787 1421 122 192 668 1245 0 0 225 490 35 95 98 97 98 96 1859 1913 .514 1.946 1.864 1.949 1.911 1.459 120 402 2.17 .91 120 2860 10300 64 76 152 164 0 1240 155 1084 1.719 1255 1099 .582 1.646 .781 .719
8 714 1334 115 175 599 1159 696 1175 116 190 581 1000 0 0 170 550 27 91 100 100 100 100 1758 1581 .517 1.935 1.721 1.843 1.813 1.369 80 336 2.356 .88 110 3010 10310 65 76 167 178 0 1178 155 1023 1.709 1038 883 .585 1.52 .773 .604
9 435 810 114 166 321 644 431 799 115 176 317 633 0 0 123 248 25 74 99 99 97 95 965 950 .498 2.006 1.997 2 1.975 1.545 120 393 2.265 .9 120 3170 10300 64 76 183 195 0 715 147 569 1.772 706 559 .564 1.763 .825 .818
10 866 1675 114 171 752 1504 829 1539 116 179 715 1368 0 0 240 470 26 73 100 100 100 100 2256 2083 .5 2 1.913 1.998 2.032 1.29 120 353 2.18 .93 120 3320 10300 64 76 198 210 0 1479 151 1328 1.766 1359 1208 .566 1.69 .821 .757
11 960 2060 112 177 848 1883 927 1691 114 192 815 1514 0 0 285 1307 25 81 100 100 100 100 2731 2329 .45 2.221 1.858 2.022 1.952 1.477 120 353 3.324 .82 120 3480 10300 64 76 214 226 -100 1819 156 1663 1.961 1493 1337 .51 1.64 .972 .714
12 1614 3182 115 191 1499 2991 1170 2643 117 204 1055 2452 0 0 1296 1788 25 92 100 100 100 99 4490 3507 .501 1.995 2.324 2.202 2.17 1.716 120 341 2.055 .82 120 3630 10300 64 76 229 241 -100 2810 169 2641 1.762 2334 2165 .568 2.052 .817 1.037
13 942 1779 118 183 824 1596 648 1216 119 197 530 1033 0 0 938 2110 28 79 100 99 99 98 2420 1563 .516 1.937 1.949 1.861 1.791 1.567 120 373 2.271 .94 120 3790 10300 64 76 245 257 -100 1571 162 1409 1.71 1074 912 .585 1.721 .774 .783
14 2341 1940 110 178 2231 1762 2249 1879 113 196 2139 1701 0 0 657 538 30 89 100 100 100 100 3993 3840 1.266 .79 .795 .789 .775 1.254 120 398 .871 .93 120 3950 10300 64 76 261 273 0 1713 157 1556 .697 1659 1502 1.434 .702 -.52 -.51
15 617 1239 109 178 508 1061 620 1204 114 196 511 1026 0 0 167 342 36 105 100 100 98 100 1569 1537 .479 2.089 2.008 2.132 2.035 1.56 80 382 2.287 .9 110 4100 10290 63 74 276 287 0 1094 157 937 1.844 1063 906 .542 1.773 .883 .826
16 1806 5166 112 188 1694 4978 1796 5178 121 227 1684 4990 0 0 327 953 69 247 100 100 100 100 6672 6674 .34 2.939 2.963 2.935 2.869 1.164 80 392 2.985 .97 110 4260 10290 63 74 292 303 0 4562 166 4396 2.595 4573 4407 .385 2.617 1.376 1.388
17 933 828 109 179 824 649 927 797 117 216 818 618 0 0 264 270 65 233 100 95 100 77 1473 1436 1.27 .788 .756 .76 .802 1.448 120 413 1.045 .86 120 4420 10300 64 76 308 320 0 731 158 573 .696 704 546 1.438 .667 -.524 -.584
18 1183 2094 106 176 1077 1918 1200 2068 112 194 1094 1892 0 0 306 514 33 182 100 100 100 100 2995 2986 .562 1.781 1.729 1.785 1.77 1.257 80 410 1.865 .95 110 4570 10290 63 74 323 334 0 1849 155 1694 1.573 1826 1671 .636 1.527 .653 .611
19 327 842 111 179 216 663 290 627 113 210 179 448 0 0 132 697 27 237 96 71 90 43 879 627 .326 3.069 2.503 2.179 2.139 2.97 32 214 12.625 .59 70 4740 10300 66 73 342 349 -100 744 158 585 2.711 554 396 .369 2.21 1.439 1.144
20 570 871 117 217 453 654 681 1021 176 283 564 804 0 0 327 507 184 248 71 71 65 65 1107 1368 .693 1.444 1.426 1.704 1.548 2.497 52 257 1.879 .85 80 4890 10260 62 70 357 365 0 769 192 578 1.275 902 710 .784 1.259 .35 .332

Total number of rows: 37632

Table truncated, full table size 8526 Kbytes.




Supplementary data files not provided
Raw data included within Sample table
Processed data included within Sample table
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