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Sample GSM82432 Query DataSets for GSM82432
Status Public on Feb 28, 2006
Title Mock control IP, embryo (1)
Sample type RNA
 
Channel 1
Source name Embryo tot. RNA extract
Organism Drosophila melanogaster
Characteristics Embryo tot. RNA extract
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name RNA, TEV eluate
Organism Drosophila melanogaster
Characteristics RNA, TEV eluate
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: RNA coimmunoprecipitation, IP Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55235.gif; format: 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 Nov 08, 2005
Last update date Feb 28, 2006
Contact name Andre Gerber
E-mail(s) andre.gerber@pharma.ethz.ch
Phone +41 44 6337378
Fax +41 44 6337364
Organization name Swiss Federal Institute of Technology
Department Institute of Pharmaceutical Science
Street address Wolfgang Pauli Str. 10, HCI H396
City ETH Hoenggerberg, Zuerich
ZIP/Postal code ZH
Country Switzerland
 
Platform ID GPL3058
Series (1)
GSE3582 RNA affinity isolation with TAP-Pum and controls

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 15532 844 210 45 15322 799 15793 896 216 46 15583 851 0 0 3686 213 54 12 100 100 100 100 16121 16434 19.176 .052 .055 .052 .051 1.351 52 420 .048 .91 90 1310 17570 56 65 42 51 0 1955 104 1850 .121 2075 1971 8.281 .126 -3.05 -2.983
2 1122 259 210 45 912 214 1091 266 214 46 881 221 0 0 222 67 52 13 100 100 100 100 1126 1102 4.262 .235 .251 .229 .237 1.486 52 414 .207 .85 90 1500 17570 56 65 61 70 0 600 104 496 .543 616 512 1.84 .581 -.88 -.784
3 631 218 213 44 418 174 658 235 802 80 445 191 0 0 177 73 5334 303 0 1 0 0 592 636 2.402 .416 .429 .401 .405 1.861 80 493 .378 .88 100 1690 17580 57 67 80 90 0 505 102 403 .964 544 442 1.037 .994 -.053 -.009
4 711 247 214 45 497 202 737 256 220 46 523 211 0 0 174 80 50 12 100 97 95 97 699 734 2.46 .406 .403 .383 .393 1.907 80 537 .371 .87 110 1870 17570 55 66 97 108 0 572 104 468 .941 593 489 1.062 .934 -.087 -.098
5 1604 2956 203 45 1401 2911 1665 3070 212 47 1462 3025 0 0 497 750 49 20 100 100 100 100 4312 4487 .481 2.078 2.069 2.201 2.001 1.618 80 494 2.113 .93 100 2060 17570 56 66 117 127 0 6845 104 6741 4.812 7109 7005 .208 4.792 2.267 2.26
6 2525 916 217 44 2308 872 2684 995 219 46 2467 951 0 0 690 237 43 20 100 100 100 100 3180 3418 2.647 .378 .385 .383 .367 1.372 80 502 .361 .96 100 2250 17570 56 66 136 146 0 2121 102 2019 .875 2304 2202 1.143 .893 -.193 -.164
7 757 392 222 45 535 347 762 385 223 46 540 340 0 0 177 62 43 12 100 100 98 100 882 880 1.542 .649 .63 .689 .674 1.61 52 394 .552 .85 90 2430 17570 56 65 154 163 0 908 104 804 1.502 892 787 .666 1.458 .587 .544
8 1606 277 215 44 1391 233 1616 274 220 46 1401 230 0 0 385 88 58 12 100 98 100 98 1624 1631 5.97 .168 .164 .155 .166 1.655 80 492 .163 .92 100 2620 17570 56 66 173 183 0 641 102 540 .388 635 533 2.578 .38 -1.366 -1.395
9 764 437 216 45 548 392 781 437 224 46 565 392 0 0 237 177 64 12 98 98 93 97 940 957 1.398 .715 .694 .697 .69 1.792 80 484 .677 .84 100 2800 17570 56 66 191 201 0 1012 104 908 1.657 1012 908 .604 1.607 .728 .684
10 682 678 216 46 466 632 715 739 224 47 499 693 0 0 193 228 54 13 95 100 93 98 1098 1192 .737 1.356 1.389 1.316 1.357 1.719 80 502 1.35 .91 100 2990 17560 55 65 210 220 0 1570 107 1464 3.141 1711 1605 .318 3.216 1.651 1.685
11 811 296 216 45 595 251 798 278 223 46 582 233 0 0 171 69 54 12 100 100 100 100 846 815 2.371 .422 .4 .425 .427 1.528 52 400 .365 .86 90 3170 17560 55 64 228 237 0 685 104 581 .977 644 540 1.024 .927 -.034 -.109
12 499 133 218 45 281 88 494 129 222 46 276 84 0 0 121 42 45 12 100 98 96 98 369 360 3.193 .313 .304 .321 .269 1.931 52 401 .233 .7 90 3350 17570 56 65 246 255 0 308 104 204 .725 299 195 1.379 .705 -.464 -.505
13 1225 737 212 48 1013 689 789 395 221 51 577 347 0 0 1100 677 52 18 87 84 71 78 1702 924 1.47 .68 .601 .634 .598 5.826 32 170 .598 .85 60 3540 17600 61 67 267 273 0 1707 111 1596 1.575 915 804 .635 1.393 .655 .478
14 558 212 208 47 350 165 434 150 223 47 226 103 0 0 356 144 111 12 76 94 50 92 515 329 2.121 .471 .456 .575 .434 3.63 52 340 .344 .73 80 3720 17560 56 64 284 292 0 491 109 382 1.092 347 239 .916 1.055 .127 .078
15 654 178 220 47 434 131 635 177 233 49 415 130 0 0 101 39 66 13 100 100 100 100 565 545 3.313 .302 .313 .298 .294 1.489 52 402 .252 .81 90 3900 17560 55 64 301 310 0 412 109 303 .699 410 301 1.431 .725 -.517 -.463
16 795 308 223 48 572 260 804 314 234 49 581 266 0 0 201 78 65 13 98 100 95 100 832 847 2.2 .455 .458 .474 .45 1.769 80 493 .411 .88 100 4090 17570 56 66 320 330 0 713 111 602 1.053 727 616 .95 1.06 .074 .084
17 1013 1737 215 48 798 1689 1035 1872 220 50 820 1824 0 0 332 506 50 13 96 100 95 100 2487 2644 .472 2.117 2.224 2.362 2.185 2.039 80 492 2.16 .9 100 4270 17560 55 65 338 348 0 4022 111 3911 4.901 4335 4224 .204 5.151 2.293 2.365
18 1006 295 226 48 780 247 977 286 231 49 751 238 0 0 256 64 57 13 100 100 100 100 1027 989 3.158 .317 .317 .322 .332 1.489 52 394 .257 .85 90 4460 17560 55 64 357 366 0 683 111 572 .733 662 551 1.364 .734 -.447 -.446
19 1106 152 231 49 875 103 1154 151 239 50 923 102 0 0 357 50 65 12 98 97 96 91 978 1025 8.495 .118 .111 .119 .119 1.747 80 494 .108 .87 100 4640 17560 55 65 375 385 0 352 113 239 .273 350 236 3.668 .256 -1.875 -1.966
20 1081 2438 235 49 846 2389 1080 2638 247 50 845 2589 0 0 262 838 82 13 100 100 97 100 3235 3434 .354 2.824 3.064 2.601 2.909 1.931 80 492 3.115 .91 100 4830 17560 55 65 394 404 0 5646 113 5532 6.539 6109 5996 .153 7.095 2.709 2.827

Total number of rows: 17664

Table truncated, full table size 3864 Kbytes.




Supplementary data files not provided

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