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Sample GSM591198 Query DataSets for GSM591198
Status Public on Dec 22, 2010
Title GIS2_delta vs. wt (3)
Sample type RNA
 
Channel 1
Source name BY4741 total RNA (WT)
Organism Saccharomyces cerevisiae
Characteristics cell line/genotype: BY4741 (WT)
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name delta Gis2 total RNA
Organism Saccharomyces cerevisiae
Characteristics cell line/genotype: delta Gis2
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol GenePix 4200A
Description Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86210.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 Sep 07, 2010
Last update date Dec 22, 2010
Contact name Andre Gerber
E-mail(s) [email protected]
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 GPL8546
Series (2)
GSE24004 Gis2 mutant versus wild-type cells
GSE24005 Gis2 studies

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 2230 987 186 91 2044 896 2309 1005 190 93 2123 914 0 0 390 165 57 24 100 100 100 100 2940 3037 2.281 .438 .431 .439 .434 1.171 120 940 .431 .98 65 2010 6835 144 157 123 136 0 2354 217 2137 1.046 2397 2180 .956 1.027 .064 .038
2 433 181 182 91 251 90 434 183 184 92 252 92 0 0 103 38 55 23 96 98 91 85 341 344 2.789 .359 .365 .353 .372 1.768 120 820 .293 .74 60 2225 6830 144 156 167 179 0 432 217 215 .855 437 219 1.169 .871 -.225 -.199
3 1589 669 180 91 1409 578 1630 688 189 92 1450 597 0 0 476 207 63 23 100 100 100 100 1987 2047 2.438 .41 .412 .403 .401 1.267 156 1140 .409 .97 70 2445 6825 142 156 210 224 0 1596 217 1379 .979 1641 1424 1.022 .982 -.031 -.026
4 340 152 190 90 150 62 337 150 191 92 147 60 0 0 98 35 58 23 80 87 61 68 212 207 2.419 .413 .408 .398 .363 2.309 120 820 .231 .56 60 2670 6830 144 156 256 268 0 363 215 148 .986 358 143 1.014 .974 -.02 -.039
5 351 135 190 91 161 44 331 131 194 92 141 40 0 0 98 33 61 23 84 71 61 42 205 181 3.659 .273 .284 .275 .292 2.739 120 820 .157 .46 60 2890 6825 143 155 300 312 0 322 217 105 .652 312 95 1.534 .677 -.617 -.563
6 316 156 185 90 131 66 320 152 190 92 135 62 0 0 84 34 56 22 83 95 60 70 197 197 1.985 .504 .459 .493 .469 2.692 120 940 .249 .49 65 3110 6825 142 155 343 356 0 372 215 157 1.202 363 148 .832 1.096 .265 .132
7 900 438 186 93 714 345 860 442 193 95 674 349 0 0 332 130 61 24 100 100 100 99 1059 1023 2.07 .483 .518 .487 .487 1.37 120 940 .445 .93 65 3335 6830 143 156 388 401 0 1045 222 823 1.153 1054 833 .868 1.235 .205 .305
8 393 167 190 92 203 75 383 165 200 95 193 73 0 0 102 41 70 25 93 92 74 75 278 266 2.707 .369 .378 .376 .368 2.173 120 820 .262 .66 60 3555 6825 143 155 433 445 0 398 219 179 .881 394 174 1.135 .902 -.182 -.148
9 458 180 190 90 268 90 453 176 191 92 263 86 0 0 101 45 59 22 99 96 95 88 358 349 2.978 .336 .327 .32 .332 1.925 120 940 .26 .7 65 3775 6825 142 155 476 489 0 429 215 215 .801 420 205 1.248 .78 -.32 -.358
10 440 168 186 93 254 75 433 162 193 94 247 69 0 0 110 38 59 23 97 91 87 79 329 316 3.387 .295 .279 .296 .301 1.972 120 820 .231 .68 60 3995 6825 143 155 521 533 0 401 222 179 .704 386 165 1.42 .666 -.506 -.586
11 6866 3205 198 96 6668 3109 7699 3601 204 98 7501 3505 0 0 2915 1373 62 24 100 100 100 100 9777 11006 2.145 .466 .467 .468 .466 1.153 156 1140 .466 .99 70 4210 6825 142 156 563 577 0 7645 229 7416 1.112 8590 8361 .899 1.115 .153 .157
12 345 147 187 91 158 56 343 145 191 92 156 54 0 0 92 32 57 22 85 85 69 58 214 210 2.821 .354 .346 .361 .326 2.429 156 1140 .226 .59 70 4435 6830 143 157 608 622 0 351 217 134 .845 346 129 1.183 .826 -.242 -.276
13 275 101 189 91 86 10 271 98 193 93 82 7 0 0 73 24 58 22 60 28 30 9 96 89 8.6 .116 .085 .257 .267 3.202 156 1272 .058 .17 75 4645 6825 141 156 649 664 0 241 217 24 .277 234 17 3.605 .204 -1.85 -2.296
14 320 117 193 93 127 24 312 118 201 95 119 25 0 0 88 27 79 29 66 40 35 11 151 144 5.292 .189 .21 .235 .232 3.339 208 1660 .097 .3 85 4875 6825 140 157 694 711 0 279 222 57 .451 281 60 2.218 .501 -1.149 -.997
15 313 110 192 92 121 18 305 110 205 96 113 18 0 0 83 25 124 32 43 29 8 2 139 131 6.722 .149 .159 .21 .211 3.6 208 1512 .076 .24 80 5095 6825 141 157 739 755 0 262 219 43 .355 262 43 2.818 .38 -1.495 -1.396
16 1044 374 197 92 847 282 1092 386 201 93 895 294 0 0 346 126 59 22 100 99 99 98 1129 1189 3.004 .333 .328 .324 .328 1.366 208 1512 .324 .94 80 5315 6820 140 156 783 799 0 892 219 673 .794 921 701 1.259 .784 -.332 -.352
17 403 149 193 91 210 58 407 145 197 93 214 54 0 0 109 38 59 22 90 83 79 61 268 268 3.621 .276 .252 .272 .272 2.374 208 1512 .202 .6 80 5540 6830 142 158 828 844 0 355 217 138 .659 346 129 1.518 .602 -.602 -.732
18 364 134 195 91 169 43 360 132 200 93 165 41 0 0 87 33 58 23 91 71 71 42 212 206 3.93 .254 .248 .246 .244 2.744 156 1272 .147 .42 75 5760 6825 141 156 872 887 0 320 217 103 .607 315 98 1.648 .593 -.72 -.755
19 421 153 193 92 228 61 411 152 201 94 218 60 0 0 116 37 61 23 93 86 84 60 289 278 3.738 .268 .275 .272 .29 2.192 120 940 .177 .55 65 5995 6820 141 154 920 933 0 365 219 146 .638 363 143 1.567 .657 -.648 -.607
20 265 106 192 89 73 17 263 104 198 91 71 15 0 0 65 24 63 23 53 35 23 12 90 86 4.294 .233 .211 .386 .297 3.149 80 560 .067 .16 50 2010 7060 191 201 125 135 0 253 212 41 .556 248 36 1.8 .504 -.848 -.989

Total number of rows: 10944

Table truncated, full table size 2337 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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