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Sample GSM39982 Query DataSets for GSM39982
Status Public on Feb 21, 2005
Title Prostate 1045
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Prostate 1045
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://jdemeter-smd.stanford.edu:8000/MicroArray/gifs/2001-06/17378.gif
 
Submission date Jan 26, 2005
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 GPL1825
Series (1)
GSE2193 Normal_human_tissues

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
VALUE same as UNF_VALUE but with flagged values removed
LOG_RAT2N_MEDIAN 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
UNF_VALUE 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

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 VALUE LOG_RAT2N_MEDIAN UNF_VALUE
1 145 117 86 83 59 34 142 96 90 88 56 13 0 0 37 72 27 30 75 25 50 18 93 69 1.735 .576 .232 .525 .886 2.9 32 188 1.469 .38 70 1210 10100 50 57 45 52 0 67 48 20 .331 55 7 3.019 .133 -1.594 -2.906 -1.594
2 149 147 80 82 69 65 136 138 83 84 56 56 0 0 34 44 22 28 100 91 75 41 134 112 1.062 .942 1 1.042 .847 1.923 12 92 2.199 .45 50 1370 10080 49 54 62 67 0 84 47 37 .541 79 32 1.847 .575 -.885 -.799 -.885
3 450 418 83 83 367 335 440 427 87 89 357 344 0 0 198 211 26 39 96 90 92 82 702 701 1.096 .913 .964 .784 .913 1.946 80 309 .974 .89 100 1490 10080 47 57 72 82 0 240 48 193 .525 245 198 1.906 .554 -.931 -.853 -.931
4 92 78 81 80 11 -2 83 77 84 84 2 -3 0 0 35 28 24 37 23 7 12 1 9 -1 null null null 1.233 1.143 5.399 80 281 1.786 .2 100 1610 10060 45 55 84 94 -50 45 46 -1 null 44 null null null null null
5 154 113 81 76 73 37 151 107 82 80 70 31 0 0 47 55 21 30 87 50 77 27 110 101 1.973 .507 .443 .572 .627 2.568 80 246 .925 .41 100 1750 10080 47 57 98 108 0 65 44 21 .291 61 18 3.433 .255 -1.779 -1.974 -1.779
6 93 94 83 77 10 17 84 82 84 85 1 5 0 0 32 49 22 49 23 15 15 6 27 6 .588 1.7 5 1.253 1.312 4.812 80 235 4.557 .21 100 1890 10080 47 57 112 122 0 54 44 10 .977 47 3 1.024 2.874 -.034 1.523 -.034
7 146 135 83 83 63 52 145 130 86 93 62 47 0 0 39 57 25 55 80 47 60 16 115 109 1.212 .825 .758 .864 1 3.234 80 226 1.742 .43 100 2030 10080 47 57 126 136 0 78 48 30 .474 75 27 2.108 .436 -1.076 -1.199 -1.076
8 214 266 85 85 129 181 219 283 87 91 134 198 0 0 54 103 25 39 96 87 92 77 310 332 .713 1.403 1.478 1.219 1.47 2.193 80 259 1.832 .74 100 2160 10080 47 57 139 149 0 153 49 104 .806 163 114 1.24 .849 -.31 -.236 -.31
9 160 110 83 82 77 28 153 102 85 84 70 20 0 0 38 43 23 29 93 43 78 18 105 90 2.75 .364 .286 .39 .486 3.425 32 147 .625 .34 60 2300 10060 47 53 155 161 0 63 47 16 .209 59 11 4.785 .164 -2.259 -2.606 -2.259
10 139 105 86 81 53 24 140 93 87 81 54 12 0 0 25 50 23 31 84 28 62 18 77 66 2.208 .453 .222 .483 .458 3.531 32 146 1.686 .24 60 2440 10060 47 53 169 175 0 60 47 14 .26 53 7 3.843 .128 -1.942 -2.969 -1.942
11 217 322 86 83 131 239 220 280 90 85 134 197 0 0 63 135 32 32 94 100 88 96 370 331 .548 1.824 1.47 1.823 1.681 2.131 52 267 2.258 .79 90 2570 10070 46 55 180 189 0 185 48 137 1.049 161 113 .954 .845 .068 -.243 .068
12 170 185 84 85 86 100 160 168 90 90 76 83 0 0 48 96 35 37 90 67 51 55 186 159 .86 1.163 1.092 .996 1.12 2.591 52 194 1.773 .51 80 2710 10060 46 54 195 203 0 106 49 57 .668 97 48 1.496 .628 -.581 -.672 -.581
13 125 129 88 80 37 49 121 121 94 88 33 41 0 0 41 55 31 37 55 55 15 26 86 74 .755 1.324 1.242 1.211 1.33 3.348 80 330 1.888 .28 100 2830 10060 45 55 206 216 0 74 46 28 .761 70 24 1.314 .714 -.394 -.486 -.394
14 181 158 88 77 93 81 180 146 93 82 92 69 0 0 43 79 28 31 95 70 80 56 174 161 1.148 .871 .75 .677 .862 2.872 80 308 1.389 .53 100 2990 10070 46 56 222 232 0 91 44 47 .501 84 40 1.998 .431 -.998 -1.214 -.998
15 187 188 92 76 95 112 188 190 94 79 96 114 0 0 45 71 30 30 92 86 73 71 207 210 .848 1.179 1.188 1.092 1.007 2.54 52 238 1.568 .54 90 3120 10060 45 54 235 244 0 108 44 64 .678 109 66 1.476 .682 -.562 -.551 -.562
16 351 604 93 74 258 530 333 581 98 81 240 507 0 0 93 191 38 34 100 100 98 98 788 747 .487 2.054 2.113 2.017 2.142 1.576 80 339 2.318 .83 110 3250 10060 44 55 247 258 0 347 43 305 1.181 334 291 .847 1.214 .24 .28 .24
17 192 210 93 78 99 132 184 198 95 84 91 120 0 0 72 83 26 34 86 88 78 76 231 211 .75 1.333 1.319 1.236 1.314 2.368 52 202 1.686 .51 80 3390 10050 45 53 263 271 0 121 45 76 .766 114 69 1.305 .758 -.384 -.4 -.384
18 207 153 90 83 117 70 204 151 95 89 114 68 0 0 68 54 29 56 90 56 85 21 187 182 1.671 .598 .596 .592 .683 2.729 80 272 .551 .54 100 3530 10060 45 55 276 286 0 88 48 40 .344 87 39 2.908 .343 -1.54 -1.545 -1.54
19 183 436 90 81 93 355 174 450 95 89 84 369 0 0 77 190 28 56 88 93 73 91 448 453 .262 3.817 4.393 3.842 4.236 2.439 80 257 4.158 .71 100 3660 10060 45 55 289 299 0 251 47 204 2.194 259 212 .456 2.525 1.133 1.336 1.133
20 277 403 93 81 184 322 275 392 99 85 182 311 0 0 96 151 49 32 91 97 78 95 506 493 .571 1.75 1.709 1.716 1.729 2.141 80 297 1.805 .66 100 3800 10060 45 55 303 313 0 232 47 185 1.006 225 179 .994 .982 .008 -.026 .008

Total number of rows: 44160

Table truncated, full table size 9334 Kbytes.




Supplementary data files not provided
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