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Sample GSM95050 Query DataSets for GSM95050
Status Public on Feb 03, 2006
Title G27-60
Sample type RNA
 
Channel 1
Source name 1 ug of Hp RNA from T=0 G27 wildtype
Organism Helicobacter pylori
Characteristics 1 ug of Hp RNA from T=0 G27 wildtype
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 1 ug of Hp RNA from T=60 G27 wildtype
Organism Helicobacter pylori
Characteristics 1 ug of Hp RNA from T=60 G27 wildtype
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Environmental conditions, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39892.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 Feb 02, 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 GPL15
Series (1)
GSE4160 Fur mutant analysis

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
1 643 684 55 65 588 619 619 591 56 65 564 526 0 0 268 334 9 16 100 100 100 100 1207 1090 .95 1.053 .933 .997 1.043 1.26 52 298 1.102 .98 80 780 12310 95 103 62 70 0 714 68 646 1.099 617 549 .91 .974 .137 -.038
2 331 231 58 67 273 164 390 252 59 69 332 185 0 0 133 76 9 18 100 96 100 96 437 517 1.665 .601 .557 .606 .637 1.464 32 220 .6 .93 70 1040 12300 94 101 88 95 0 241 70 171 .627 263 193 1.594 .582 -.673 -.781
3 217 270 57 67 160 203 130 163 58 68 73 96 0 0 165 218 11 24 100 100 96 81 363 169 .788 1.269 1.315 1.28 1.294 1.658 32 220 1.398 .97 70 1290 12300 94 101 113 120 0 282 70 212 1.325 170 100 .755 1.373 .406 .458
4 70 68 54 63 16 5 58 65 74 91 4 2 0 0 40 20 181 259 0 0 0 0 21 6 3.2 .313 .5 1.201 1.208 3.57 80 648 1.331 .96 110 1510 12310 93 104 133 144 -50 71 66 5 .326 68 2 3.065 .522 -1.616 -.938
5 69 69 53 60 16 9 55 67 72 89 2 7 0 0 46 21 181 259 5 0 0 0 25 9 1.778 .563 3.5 1.289 1.083 4.428 80 648 .452 .36 110 1750 12310 93 104 157 168 -50 72 63 9 .587 70 7 1.703 3.655 -.768 1.87
6 64 73 54 63 10 10 57 68 58 65 3 5 0 0 24 23 25 21 15 16 7 6 20 8 1 1 1.667 1.007 .893 3.62 80 649 1.718 .49 110 1990 12310 93 104 181 192 -50 76 66 10 1.044 71 5 .958 1.74 .062 .799
7 265 188 54 63 211 125 302 194 55 64 248 131 0 0 81 63 9 18 100 100 100 83 336 379 1.688 .592 .528 .547 .546 1.372 12 90 .636 .91 50 2230 12290 94 99 208 213 0 196 66 131 .619 203 137 1.617 .552 -.693 -.858
8 387 235 58 67 329 168 390 226 58 67 332 159 0 0 47 70 10 16 100 100 100 100 497 491 1.958 .511 .479 .47 .491 1.624 12 98 .548 .9 50 2470 12300 95 100 232 237 0 245 70 175 .533 236 166 1.875 .5 -.907 -1
9 765 741 56 61 709 680 789 770 56 63 733 709 0 0 312 338 9 16 100 100 100 100 1389 1442 1.043 .959 .967 .93 .921 1.171 32 220 .982 .98 70 2710 12290 93 100 255 262 0 774 64 710 1.001 804 740 .999 1.01 .002 .014
10 135 110 57 63 78 47 95 85 58 65 38 22 0 0 85 69 14 18 78 53 62 40 125 60 1.66 .603 .579 .771 .722 3.162 32 236 .012 .57 70 2960 12320 96 103 280 287 0 115 66 49 .629 89 23 1.589 .605 -.668 -.726
11 260 183 58 64 202 119 269 172 58 65 211 108 0 0 73 73 8 15 100 100 100 83 321 319 1.697 .589 .512 .514 .633 1.648 12 62 .625 .88 40 3190 12300 96 100 305 309 0 191 67 124 .615 180 113 1.626 .534 -.701 -.904
12 279 211 55 61 224 150 306 221 55 63 251 160 0 0 94 74 8 16 100 100 100 96 374 411 1.493 .67 .637 .645 .684 1.459 32 217 .681 .93 70 3430 12280 92 99 327 334 0 220 64 157 .699 231 167 1.43 .666 -.516 -.587
13 275 254 55 62 220 192 306 252 55 62 251 190 0 0 78 82 10 14 100 100 100 100 412 441 1.146 .873 .757 .864 .882 1.382 12 98 .881 .92 50 3660 12290 94 99 351 356 0 265 65 200 .911 263 198 1.097 .79 -.134 -.339
14 307 516 58 64 249 452 215 300 58 66 157 236 0 0 231 458 9 17 100 100 93 100 701 393 .551 1.815 1.503 1.772 1.749 1.483 32 170 1.935 .98 60 3900 12290 94 100 375 381 0 539 67 472 1.895 313 246 .528 1.57 .923 .65
15 258 205 59 69 199 136 219 206 485 458 160 137 0 0 129 80 3553 2962 0 0 0 0 335 297 1.463 .683 .856 .704 .686 1.978 32 170 .662 .94 60 4160 12290 94 100 401 407 0 214 72 142 .714 215 143 1.401 .894 -.487 -.162
16 85 108 54 60 31 48 58 77 54 62 4 17 0 0 85 118 9 15 36 52 21 25 79 21 .646 1.548 4.25 1.868 1.987 3.418 80 648 1.453 .92 110 4380 12290 91 102 420 431 -50 113 63 50 1.617 80 18 .619 4.438 .693 2.15
17 188 207 54 60 134 147 208 171 56 63 154 111 0 0 94 122 9 19 100 91 100 75 281 265 .912 1.097 .721 .978 .866 1.887 12 68 1.256 .84 40 4630 12300 96 100 449 453 0 216 63 153 1.145 179 116 .873 .753 .196 -.41
18 373 274 60 77 313 197 399 291 62 73 339 214 0 0 118 90 13 15 100 100 100 91 510 553 1.589 .629 .631 .566 .595 1.612 12 42 .661 .96 40 770 12560 122 126 63 67 0 286 80 206 .657 304 223 1.522 .659 -.606 -.601
19 129 147 57 64 72 83 86 111 58 67 29 47 0 0 102 109 8 16 91 91 75 75 155 76 .867 1.153 1.621 1.489 1.192 1.734 12 104 1.146 .93 50 1030 12550 120 125 88 93 0 153 67 87 1.204 116 49 .831 1.692 .267 .759
20 70 76 55 63 15 13 61 72 56 65 6 9 0 0 33 24 9 16 40 35 16 10 28 15 1.154 .867 1.5 1.336 1.254 3.682 80 656 1.016 .47 110 1270 12550 117 128 109 120 -50 79 66 14 .905 75 9 1.105 1.566 -.144 .647

Total number of rows: 4608

Table truncated, full table size 969 Kbytes.




Supplementary data files not provided
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