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Sample GSM6255 Query DataSets for GSM6255
Status Public on Apr 15, 2004
Title AML 92
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name AML 92
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=4.544.63
Lot batch = shcz209
 
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
1 197 302 0 193 143 105 391 252 898 801 691 788 0 469 144 97 559 118 977 1095 843 961 .92 100 0 1.955 2.097 3.726 3.364 22 1 58 25 .315 .258 3.179 3.508 1.923 3.876 4.278 3.021 1053 888 396 80 1880 8130 48 58 35 45 1.955
2 341 447 0 300 115 106 57 461 146 52 41 135 0 42 96 94 29 115 63 178 50 165 .53 90 0 -2.862 -2.77 .116 .105 100 94 65 38 8.865 7.27 .113 .12 2.123 .138 .147 .081 513 382 289 52 2040 8130 48 57 51 60 -2.862
3 427 535 0 307 111 108 30 512 245 156 124 213 0 100 94 89 29 109 190 299 151 260 .85 90 0 -1.428 -1.498 .292 .301 100 100 96 82 3.282 2.691 .305 .29 1.751 .372 .354 .271 668 551 289 52 2170 8130 48 57 64 73 -1.428
4 91 200 0 82 111 109 28 102 414 322 281 373 0 196 96 92 32 112 393 505 343 455 .71 90 0 1.945 1.913 3.268 3.417 78 67 98 96 .317 .26 3.157 3.088 2.536 3.85 3.766 3.596 424 372 337 52 2320 8120 47 56 79 88 1.945
5 35 143 0 42 114 108 32 36 116 22 14 108 0 57 97 94 31 115 27 141 17 132 .12 100 -50 -1.036 .831 .737 52 26 26 8 1.636 1.342 .611 .4 3.536 .745 .488 1.447 58 49 428 80 2480 8130 48 58 95 105 -.424
6 70 175 0 45 110 105 28 70 125 30 24 119 0 40 99 95 28 116 37 152 29 145 .23 60 0 -.936 -1.258 .5 .606 81 62 46 18 2.333 1.913 .429 .343 3.098 .523 .418 .326 100 94 126 32 2620 8110 48 54 111 117 -.936
7 41 143 0 51 105 102 27 52 166 76 61 151 0 56 94 90 29 110 93 202 74 184 .38 100 0 .834 .859 1.306 1.521 67 37 76 53 .684 .561 1.462 1.488 4.087 1.782 1.814 1.881 128 102 370 80 2760 8130 48 58 123 133 .834
8 80 185 0 65 111 105 29 83 102 17 14 99 0 29 90 85 27 104 21 124 17 121 .15 60 0 -2.001 -2.228 .385 .375 75 59 31 12 4.882 4.004 .205 .175 3.288 .25 .213 .113 100 94 144 32 2920 8140 51 57 141 147 -2.001
9 9 112 0 27 107 103 27 14 101 13 9 97 0 28 91 88 27 107 16 123 11 118 .25 100 -50 .286 1.058 1.156 26 8 31 10 1.077 .883 .929 1 3.986 1.132 1.22 1.535 27 18 348 80 3060 8130 48 58 153 163 .179
10 87 191 0 45 107 104 32 85 108 20 18 106 0 33 92 88 27 107 24 132 22 129 .22 90 0 -1.801 -1.987 .35 .393 88 61 38 15 4.25 3.485 .235 .207 2.768 .287 .252 .153 105 105 323 52 3200 8120 47 56 167 176 -1.801
11 54 159 0 57 114 105 38 65 101 18 11 94 0 35 87 83 26 101 22 123 13 115 .14 70 0 -1.566 -2.009 .277 .376 65 40 25 12 3.611 2.961 .277 .204 3.721 .338 .248 .116 83 65 199 32 3360 8110 47 54 184 191 -1.566
12 179 282 0 86 108 103 33 181 184 94 91 181 0 60 91 90 28 110 115 224 111 221 .51 70 0 -.659 -.69 .429 .599 96 90 78 71 1.926 1.579 .519 .508 3.098 .633 .62 .34 275 270 201 32 3480 8130 49 56 196 203 -.659
13 82 182 0 269 103 100 28 134 115 25 20 110 0 35 92 90 28 110 30 140 24 134 .13 70 -100 -1.749 .4 .42 81 65 40 18 5.36 4.395 .187 .244 2.604 .228 .297 .031 159 102 212 32 3630 8140 50 57 211 218 -2.136
14 7 108 0 34 104 101 25 15 92 3 -1 88 0 28 91 89 27 109 4 112 107 .03 100 -50 1.022 .974 31 16 20 3 5 4.1 .2 3.999 .244 1.415 18 6 350 80 3790 8120 47 57 226 236 -2.036
15 118 221 0 101 105 103 24 129 592 505 474 561 0 308 89 87 25 106 616 722 578 684 .82 100 0 2.255 2.292 4.392 4.246 85 77 100 100 .255 .209 3.915 4.017 2.375 4.774 4.899 3.87 634 592 315 80 3930 8110 46 56 240 250 2.255
16 938 1042 0 550 108 104 30 956 853 763 791 881 0 348 93 90 27 110 930 1040 965 1074 .92 100 0 -.039 .04 .862 .814 96 95 100 98 1.253 1.027 .798 .843 1.48 .973 1.028 .727 1719 1729 321 80 4080 8120 47 57 255 265 -.039
17 215 315 0 259 105 100 30 291 916 824 559 651 0 620 95 92 30 112 1005 1117 682 794 .85 110 0 1.788 1.665 3.226 3.152 97 91 100 100 .353 .29 2.832 2.6 1.714 3.453 3.171 3.1 1115 774 422 80 4220 8120 46 57 268 279 1.788
18 25 125 0 40 103 100 31 29 89 0 -2 87 0 26 91 89 28 109 0 109 106 .05 100 -50 .711 .903 43 18 15 2 2.841 .18 29 23 369 80 4370 8120 47 57 284 294
19 87 202 0 43 121 115 42 94 121 28 26 119 0 34 90 93 27 113 34 148 32 145 .25 50 0 -1.461 -1.456 .289 .312 91 50 50 25 3.357 2.753 .298 .299 4.22 .363 .364 .171 122 113 76 12 4500 8100 47 52 299 304 -1.461
20 14 117 0 38 107 103 36 27 101 12 6 95 0 32 91 89 26 109 15 123 7 116 .16 100 -50 -.936 1.062 .798 31 11 26 13 2.25 1.845 .444 .429 3.625 .542 .523 .736 39 20 368 80 4660 8120 47 57 313 323 -.884

Total number of rows: 43008

Table truncated, full table size 8808 Kbytes.




Supplementary data files not provided

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