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Sample GSM6254 Query DataSets for GSM6254
Status Public on Apr 15, 2004
Title AML 36
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 36
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=670650LaserPower=4.524.72
Lot batch = shcz208
 
Submission date May 07, 2003
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) pollack1@stanford.edu
Phone 650-736-1987
Organization name Stanford University
Department Pathology
Lab Pollack Lab
Street address 269 Campus Drive, CCSR3245A
City Stanford
State/province CA
ZIP/Postal code 94305-5176
Country USA
 
Platform ID GPL318
Series (1)
GSE425 Acute myeloid leukemia study

Data table header descriptions
ID_REF
CH1D_MEDIAN Median spot pixel intensity at Channel 1 with the median-background subtracted (CH1I_MEDIAN - CH1B_MEDIAN)
CH1I_MEDIAN Median spot pixel intensity at Channel 1
CH1_PER_SAT Percentage of spot pixels at Channel 1 that are saturated
CH1I_SD Standard deviation of the spot intensity at Channel 1
CH1B_MEAN Mean spot background in Channel 1
CH1B_MEDIAN Median spot background intensity in Channel 1
CH1B_SD Standard deviation of the spot background intensity in Channel 1
CH1D_MEAN Mean Channel 1 intensity with the median-background subtracted (CH1I_MEAN - CH1B_MEDIAN)
CH2I_MEAN Mean spot pixel intensity at Channel 2
CH2D_MEAN Mean spot pixel intensity at Channel 2 with the median-background subtracted (CH2I_MEAN - CH2B_MEDIAN)
CH2D_MEDIAN Median spot pixel intensity at Channel 2 with the median-background subtracted (CH2I_MEDIAN - CH2B_MEDIAN)
CH2I_MEDIAN Median spot pixel intensity at Channel 2
CH2_PER_SAT Percentage of spot pixels at Channel 2 that are saturated
CH2I_SD Standard deviation of the spot pixel intensity at at Channel 2
CH2B_MEAN Mean spot background intensity in Channel 2
CH2B_MEDIAN Median spot background intensity in Channel 2
CH2B_SD Standard deviation of the spot background intensity in Channel 2
CH2BN_MEDIAN Normalized value of median Channel 2 background (CH2B_MEDIAN/Normalization factor)
CH2DN_MEAN Normalized value of mean Channel 2 intensity with normalized background subtracted (CH2IN_MEAN - CH2BN)
CH2IN_MEAN Normalized value of mean Channel 2 intensity (CH2I_MEAN/Normalization factor)
CH2DN_MEDIAN Normalized value of median Channel 2 intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN)
CH2IN_MEDIAN Normalized value of median Channel 2 intensity (CH2_MEDIAN/Normalization factor)
CORR Coefficient of determination for the current regression value
DIAMETER Diameter in µm of the spot indicator
FLAG Type of flag associated with a spot (default=0)
VALUE same as UNF_VALUE but with flagged values removed
LOG_RAT2N_MEDIAN Log (base 2) of the ratio of the medians of Channel 2 to Channel 1 [log (base 2) (RAT2N_MEDIAN)]
PIX_RAT2_MEAN Geometric mean of the pixel-by-pixel ratios of Channel 2 to Channel 1 pixel intensities, with the median background subtracted
PIX_RAT2_MEDIAN Median of pixel by-pixel ratios of Channel 2 to Channel 1 pixel intensities, with the median background subtracted
PERGTBCH1I_1SD Percentage of spot pixels with intensities more than one standard deviation above the background pixel intensity, at Channel 1
PERGTBCH1I_2SD
PERGTBCH2I_1SD Percentage of spot pixels with intensities more than one standard deviation above the background pixel intensity, at Channel 2
PERGTBCH2I_2SD Percentage of spot pixels with intensities more than two standard deviations above the background pixel intensity, at Channel 1
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
RAT1N_MEAN Ratio of the means of Channel 1 intensity to normalized Channel 2 intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized
RAT2_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 2/Channel 1 ratio, (CH2I_MEAN - CH2B_MEDIAN)/(CH1_MEAN - CH1B_MEDIAN) or Red/Green ratio
RAT2_MEDIAN Ratio of the median intensities of each spot for each wavelength, with the median background subtracted
RAT2_SD Standard deviation of pixel intensity ratios
RAT2N_MEAN Channel 2/Channel 1 ratio normalized, RAT2N_MEAN/Normalization factor or Red/Green mean ratio normalized
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2N_MEDIAN/Normalization factor or Red/Green median ratio normalized
REGR Regression ratio
SUM_MEAN Sum of the arithmetic mean intensities for each wavelength, with the median background subtracted (CH1D_MEAN + CH2D_MEAN)
SUM_MEDIAN Sum of the median intensities for each wavelength, with the median-background subtracted (CH1D_MEDIAN + CH2D_MEDIAN)
TOT_BPIX Total number of background pixels
TOT_SPIX Total number of signal (spot) pixels
X_COORD X-coordinate in µm of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image
Y_COORD Y-coordinate in µm of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize)
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize)
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize)
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize)
UNF_VALUE aka LOG_RAT2N_MEAN, or Log (base 2) of the ratio of the mean of Channel 2 to Channel 1 [log (base 2) (RAT2N_MEAN)]

Data table
ID_REF CH1D_MEDIAN CH1I_MEDIAN CH1_PER_SAT CH1I_SD CH1B_MEAN CH1B_MEDIAN CH1B_SD CH1D_MEAN CH2I_MEAN CH2D_MEAN CH2D_MEDIAN CH2I_MEDIAN CH2_PER_SAT CH2I_SD CH2B_MEAN CH2B_MEDIAN CH2B_SD CH2BN_MEDIAN CH2DN_MEAN CH2IN_MEAN CH2DN_MEDIAN CH2IN_MEDIAN CORR DIAMETER FLAG VALUE LOG_RAT2N_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN PERGTBCH1I_1SD PERGTBCH1I_2SD PERGTBCH2I_1SD PERGTBCH2I_2SD RAT1_MEAN RAT1N_MEAN RAT2_MEAN RAT2_MEDIAN RAT2_SD RAT2N_MEAN RAT2N_MEDIAN REGR SUM_MEAN SUM_MEDIAN TOT_BPIX TOT_SPIX X_COORD Y_COORD TOP BOT LEFT RIGHT UNF_VALUE
1 208 287 0 150 82 79 22 248 2669 2588 2288 2369 0 1370 85 81 25 95 3045 3140 2692 2787 .88 90 0 3.618 3.694 11.128 10.289 100 98 100 100 .096 .081 10.435 11 1.627 12.277 12.941 9.993 2836 2496 317 52 2120 8080 55 64 39 48 3.618
2 460 539 0 296 83 79 25 540 314 230 209 293 0 123 86 84 26 99 271 369 246 345 .89 80 0 -.997 -.904 .421 .444 100 100 100 96 2.348 1.996 .426 .454 1.663 .501 .535 .398 770 669 246 52 2270 8080 56 64 55 63 -.997
3 404 489 0 229 89 85 24 459 379 297 269 351 0 139 87 82 27 96 349 446 316 413 .88 80 0 -.394 -.352 .662 .65 100 100 100 100 1.545 1.314 .647 .666 1.636 .761 .783 .609 756 673 237 52 2410 8080 56 64 69 77 -.394
4 180 272 0 232 528 92 4345 263 160 67 50 143 0 73 1058 93 6301 109 79 188 59 168 .95 90 0 -1.738 -1.614 .29 .295 0 0 0 0 3.925 3.337 .255 .278 2.294 .3 .327 1.249 330 230 307 52 2550 8080 55 64 82 91 -1.738
5 40 128 0 39 93 88 27 50 108 22 11 97 0 41 89 86 28 101 26 127 13 114 .11 70 0 -.95 -1.628 .673 .719 65 40 34 12 2.273 1.932 .44 .275 4.192 .518 .324 .547 72 51 195 32 2690 8060 54 61 97 104 -.95
6 47 129 0 53 85 82 21 59 139 54 53 138 0 40 87 85 27 100 64 164 62 162 .39 70 0 .107 .408 1.078 1.258 71 56 68 46 1.093 .929 .915 1.128 3.042 1.077 1.327 .778 113 100 206 32 2860 8080 56 63 114 121 .107
7 53 135 0 92 87 82 25 82 199 116 77 160 0 148 86 83 27 98 136 234 91 188 .75 90 0 .735 .773 1.144 1.138 78 50 82 67 .707 .601 1.415 1.453 2.646 1.664 1.709 1.794 198 130 340 52 3000 8080 55 64 127 136 .735
8 51 132 0 74 84 81 21 75 129 49 39 119 0 51 85 80 27 94 58 152 46 140 .4 70 0 -.38 -.153 .539 .507 71 53 62 43 1.531 1.301 .653 .765 5.305 .769 .9 .616 124 90 198 32 3160 8080 56 63 144 151 -.38
9 8 93 0 22 86 85 22 8 96 10 7 93 0 35 89 86 30 101 12 113 8 109 .04 100 -50 .042 1.712 1.45 22 3 28 7 .8 .68 1.25 .875 3.866 1.471 1.029 .059 18 15 339 80 3300 8080 55 65 157 167 .556
10 106 194 0 71 90 88 23 115 94 5 2 91 0 27 93 89 33 105 6 111 2 107 .05 100 0 -4.289 -5.493 .218 .159 91 88 16 3 23 19.55 .043 .019 4.788 .051 .022 .04 120 108 333 80 3440 8080 55 65 171 181 -4.289
11 28 113 0 48 89 85 24 39 91 5 1 87 0 27 90 86 31 101 6 107 1 102 .13 100 -50 -4.573 .543 .558 56 27 15 5 7.8 6.63 .128 .036 3.831 .151 .042 .282 44 29 339 80 3600 8080 55 65 187 197 -2.729
12 128 216 0 119 91 88 34 152 167 81 66 152 0 77 88 86 28 101 95 196 78 179 .74 80 0 -.674 -.721 .417 .479 88 78 71 59 1.877 1.595 .533 .516 2.95 .627 .607 .56 233 194 244 52 3730 8080 56 64 201 209 -.674
13 63 149 0 54 92 86 34 71 139 53 38 124 0 67 88 86 27 101 62 164 45 146 .51 80 0 -.187 -.495 .681 .654 67 44 61 32 1.34 1.139 .746 .603 3.417 .878 .71 1.092 124 101 260 52 3880 8080 56 64 216 224 -.187
14 10 96 0 28 88 86 22 13 87 2 2 87 0 27 87 85 30 100 2 102 2 102 .06 100 -50 -2.087 .722 .625 30 12 10 2 6.5 5.525 .154 .2 4.971 .181 .235 3.579 15 12 334 80 4030 8080 55 65 230 240 -2.466
15 46 128 0 74 86 82 22 59 1662 1574 980 1068 0 1586 90 88 30 104 1852 1955 1153 1256 .83 100 0 4.972 4.648 22.308 23.203 65 50 100 100 .037 .032 26.678 21.304 1.917 31.386 25.064 26.226 1633 1026 339 80 4170 8080 55 65 244 254 4.972
16 238 322 0 694 87 84 23 548 920 829 434 525 0 885 92 91 30 107 975 1082 511 618 .94 100 0 .832 1.101 1.936 1.648 90 86 98 97 .661 .562 1.513 1.824 2.278 1.78 2.145 1.38 1377 672 334 80 4320 8080 55 65 259 269 .832
17 137 224 0 158 90 87 23 197 856 767 541 630 0 690 93 89 30 105 902 1007 636 741 .88 90 0 2.195 2.216 3.805 3.692 96 94 100 98 .257 .218 3.893 3.949 1.997 4.58 4.646 4.311 964 678 280 52 4460 8070 54 63 273 282 2.195
18 22 110 0 36 91 88 25 29 94 6 4 92 0 30 91 88 28 104 7 111 5 108 .03 100 -50 -2.225 .894 .865 47 23 22 6 4.833 4.108 .207 .182 5.07 .243 .214 .874 35 26 398 80 4620 8080 55 65 289 299 -2.039
19 54 147 0 38 101 93 31 53 112 20 11 103 0 40 97 92 28 108 24 132 13 121 .23 50 0 -1.172 -2.061 .886 .998 58 41 41 16 2.65 2.253 .377 .204 5.189 .444 .24 .514 73 65 72 12 4760 8050 54 59 305 310 -1.172
20 8 99 0 28 93 91 25 12 101 11 6 96 0 29 93 90 28 106 13 119 7 113 .08 100 -50 -.181 1.195 1.286 26 10 25 5 1.091 .927 .917 .75 4.974 1.078 .882 1.517 23 14 402 80 4910 8080 55 65 318 328 .109

Total number of rows: 43008

Table truncated, full table size 8743 Kbytes.




Supplementary data files not provided

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