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Sample GSM591199 Query DataSets for GSM591199
Status Public on Dec 22, 2010
Title GIS2_delta vs. wt (2)
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/2010-01/86209.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 1327 728 77 49 1250 679 1333 783 84 50 1256 734 0 0 634 248 55 11 100 100 97 100 1929 1990 1.841 .543 .584 .551 .569 1.437 156 1272 .464 .9 75 2140 6865 149 164 148 163 0 1348 91 1257 1.006 1450 1359 .994 1.082 .008 .114
2 199 101 74 49 125 52 198 101 82 50 124 52 0 0 56 23 85 14 72 95 20 85 177 176 2.404 .416 .419 .408 .389 2.031 120 940 .329 .71 65 2350 6855 148 161 191 204 0 187 91 96 .77 187 96 1.298 .777 -.377 -.365
3 331 159 73 47 258 112 325 161 78 49 252 114 0 0 70 30 29 11 100 100 100 100 370 366 2.304 .434 .452 .435 .446 1.396 120 940 .405 .89 65 2575 6850 147 160 236 249 0 294 87 207 .804 298 211 1.244 .838 -.315 -.256
4 82 50 74 47 8 3 78 49 76 48 4 2 0 0 29 12 25 11 25 20 8 6 11 6 2.667 .375 .5 .441 .476 4.195 316 2384 .017 .03 100 2790 6855 145 165 276 296 -50 93 87 6 .694 91 4 1.44 .926 -.526 -.111
5 125 57 78 48 47 9 110 54 84 49 32 6 0 0 69 13 37 11 45 38 21 21 56 38 5.222 .191 .188 .239 .208 4.528 80 656 .05 .18 55 3020 6840 146 157 326 337 0 106 89 17 .355 100 11 2.82 .347 -1.496 -1.526
6 118 66 80 48 38 18 115 66 85 49 35 18 0 0 42 15 30 11 53 63 27 35 56 53 2.111 .474 .514 .399 .356 2.679 80 656 .121 .22 55 3230 6855 149 160 368 379 0 122 89 33 .877 122 33 1.14 .952 -.189 -.071
7 241 127 77 49 164 78 253 126 84 50 176 77 0 0 96 45 55 12 83 91 69 84 242 253 2.103 .476 .438 .48 .452 2.017 156 1140 .404 .84 70 3450 6855 148 162 411 425 0 235 91 144 .881 233 143 1.135 .81 -.183 -.304
8 157 82 74 49 83 33 156 81 82 51 82 32 0 0 41 19 44 14 79 80 44 56 116 114 2.515 .398 .39 .386 .374 2.328 120 820 .26 .55 60 3675 6850 148 160 457 469 0 152 91 61 .736 150 59 1.358 .723 -.442 -.469
9 128 64 78 49 50 15 124 63 82 50 46 14 0 0 37 14 30 12 68 54 36 24 65 60 3.333 .3 .304 .341 .333 3.343 120 940 .149 .35 65 3885 6860 149 162 498 511 0 119 91 28 .555 117 26 1.8 .564 -.848 -.827
10 126 62 78 47 48 15 121 61 89 49 43 14 0 0 38 14 67 13 30 50 2 18 63 57 3.2 .313 .326 .315 .284 3.15 120 820 .069 .16 60 4115 6850 148 160 545 557 0 115 87 28 .579 113 26 1.728 .603 -.789 -.73
11 964 540 78 48 886 492 1034 566 81 49 956 518 0 0 253 138 27 13 100 100 100 100 1378 1474 1.801 .555 .542 .556 .55 1.218 120 940 .547 .98 65 4330 6850 147 160 587 600 0 1000 89 911 1.028 1048 959 .973 1.003 .04 .005
12 96 56 75 47 21 9 93 54 78 48 18 7 0 0 31 17 24 11 39 38 19 21 30 25 2.333 .429 .389 .523 .484 3.134 316 2384 .127 .19 100 4545 6855 145 165 627 647 -50 104 87 17 .794 100 13 1.26 .72 -.334 -.474
13 126 65 78 47 48 18 121 64 81 48 43 17 0 0 37 15 27 11 66 64 36 33 66 60 2.667 .375 .395 .415 .429 3.381 208 1512 .146 .34 80 4770 6855 147 163 674 690 0 120 87 33 .694 119 31 1.44 .732 -.526 -.45
14 197 103 79 48 118 55 188 103 84 49 109 55 0 0 62 25 35 11 90 96 77 90 173 164 2.145 .466 .505 .52 .469 2.14 208 1660 .281 .65 85 4985 6860 147 164 716 733 0 191 89 102 .863 191 102 1.159 .934 -.212 -.098
15 139 70 80 48 59 22 139 68 83 49 59 20 0 0 39 18 26 11 78 69 56 44 81 79 2.682 .373 .339 .352 .381 2.992 256 1924 .203 .43 90 5200 6855 146 164 759 777 0 130 89 41 .69 126 37 1.448 .628 -.534 -.672
16 488 209 85 48 403 161 506 213 97 50 421 165 0 0 187 79 106 17 95 99 78 96 564 586 2.503 .4 .392 .391 .397 1.431 208 1512 .245 .73 80 5425 6850 146 162 805 821 0 387 89 298 .74 394 306 1.352 .726 -.435 -.463
17 195 96 85 48 110 48 189 95 88 48 104 47 0 0 56 25 28 11 94 90 83 81 158 151 2.292 .436 .452 .434 .429 2.289 208 1512 .356 .73 80 5645 6860 148 164 849 865 0 178 89 89 .808 176 87 1.238 .837 -.308 -.257
18 120 58 88 47 32 11 116 55 91 50 28 8 0 0 33 15 31 25 46 17 19 0 43 36 2.909 .344 .286 .443 .385 3.524 156 1140 .734 .46 70 5860 6855 148 162 893 907 0 107 87 20 .637 102 15 1.571 .529 -.652 -.919
19 154 70 89 48 65 22 149 70 92 49 60 22 0 0 40 17 28 13 80 70 55 40 87 82 2.955 .338 .367 .337 .326 2.65 120 940 .164 .34 65 6080 6860 149 162 937 950 0 130 89 41 .627 130 41 1.596 .679 -.674 -.559
20 119 61 84 49 35 12 110 61 128 54 26 12 0 0 38 15 440 41 0 2 0 0 47 38 2.917 .343 .462 .462 .459 3.292 120 820 .038 .36 60 2125 7080 194 206 147 159 0 113 91 22 .635 113 22 1.575 .855 -.655 -.227

Total number of rows: 10944

Table truncated, full table size 2285 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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