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Sample GSM72140 Query DataSets for GSM72140
Status Public on Aug 27, 2005
Title CLL-53
Sample type RNA
 
Channel 1
Source name Lymphopool
Organism Homo sapiens
Characteristics Lymphopool
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name CLL-53
Organism Homo sapiens
Characteristics CLL-53
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2668.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Aug 26, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL2793
Series (1)
GSE3211 Relation of Gene Expression Phenotype to Immunoglobulin Mutation Genotype in B Cell Chronic Lymphocytic Leukemia

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Uncorrected Cy3 mean pixel intensity.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_MEAN Uncorrected Cy3 mean pixel intensity.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_MEDIAN Median intensities of background pixels of Cy3.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2B_MEDIAN Median intensities of background pixels of Cy3.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1D_MEAN The mean feature pixel intensity with the median background subtracted (channel 1).; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN The mean feature pixel intensity with the median background subtracted (channel 2).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_MEAN Mean intensities of background pixels of Cy3.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN Mean intensities of background pixels of Cy5.; Type: integer; Scale: linear_scale; 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
PIX_RAT2_MEDIAN Contains median of Ch2PI-CH2B/Ch1PI-CH1B where Ch1PI & Ch2PI represent single pixel intensities.; Type: float; Scale: linear_scale
TOT_SPIX Count of the number of pixels in the spot.; Type: integer; Scale: linear_scale
TOT_BPIX 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
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 User defined spot flag (default 0).; 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
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
VALUE same as UNF_VALUE but with flagged values removed
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 CH1B_MEAN CH2B_MEAN PERGTBCH1I_1SD PERGTBCH2I_1SD PIX_RAT2_MEDIAN TOT_SPIX TOT_BPIX REGR CORR TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN RAT1N_MEAN VALUE UNF_VALUE
1 164 174 133 133 31 41 143 142 23 28 1.164 177 1164 .425 .473 46 61 66 81 0 145 111 34 1.099 .91 .136 .136
2 1642 4749 131 140 1511 4609 138 148 61 63 2.946 177 928 0 0 46 61 84 99 0 3946 116 3830 2.535 .395 1.342 1.342
3 2669 11687 144 144 2525 11543 151 155 68 74 4.281 177 928 0 0 46 61 101 116 0 9711 120 9591 3.799 .263 1.925 1.925
4 3254 1507 152 151 3102 1356 163 162 62 63 .436 177 919 0 0 46 61 119 134 0 1252 125 1127 .363 2.753 -1.461 -1.461
5 5065 8259 160 161 4905 8098 171 170 64 67 1.571 177 906 0 0 46 61 136 151 0 6863 134 6729 1.372 .729 .456 .456
6 2226 4040 153 163 2073 3877 164 171 61 62 1.676 177 896 1.714 2.129 46 61 154 169 0 3357 135 3222 1.554 .643 .636 .636
7 4834 3973 153 157 4681 3816 161 165 67 64 .821 177 896 0 0 46 61 171 186 0 3301 130 3171 .677 1.476 -.562 -.562
8 2059 2085 155 144 1904 1941 163 158 60 59 .933 177 886 .897 .879 46 61 189 204 0 1733 120 1613 .847 1.181 -.239 -.239
9 2558 1304 155 145 2403 1159 165 157 61 56 .494 177 896 .434 .881 46 61 206 221 0 1084 120 963 .401 2.495 -1.319 -1.319
10 1768 1173 156 148 1612 1025 166 159 53 53 .633 177 928 .551 .851 45 60 224 239 0 975 123 852 .528 1.893 -.92 -.92
11 4031 7253 155 146 3876 7107 165 159 62 75 1.786 177 928 0 0 45 60 241 256 0 6027 121 5905 1.524 .656 .607 .607
12 3979 4177 159 149 3820 4028 170 159 57 58 1.057 177 928 0 0 45 60 259 274 0 3471 124 3347 .876 1.141 -.191 -.191
13 326 376 159 154 167 222 169 164 36 35 1.359 177 919 1.035 .817 45 60 276 291 0 312 128 184 1.105 .905 .144 .144
14 1909 5366 158 157 1751 5209 169 166 56 68 2.896 177 905 0 0 45 60 294 309 0 4459 130 4328 2.472 .405 1.306 1.306
15 3130 13987 159 158 2971 13829 169 165 70 82 3.989 177 896 0 0 45 60 311 326 0 11622 131 11491 3.868 .259 1.951 1.951
16 3961 1707 163 163 3798 1544 176 167 62 62 .403 177 896 8.585 4.278 45 60 329 344 0 1418 135 1283 .338 2.96 -1.566 -1.566
17 5711 8719 163 158 5548 8561 177 163 75 81 1.519 177 896 0 0 45 60 346 361 0 7245 131 7114 1.282 .78 .359 .359
18 2502 4296 159 151 2343 4145 171 158 62 68 1.659 177 928 0 0 44 59 364 379 0 3570 125 3444 1.47 .68 .556 .556
19 5416 4335 163 149 5253 4186 172 158 67 65 .805 177 928 0 0 44 59 381 396 0 3602 124 3478 .662 1.51 -.595 -.595
20 2481 2410 166 145 2315 2265 180 158 62 61 .923 177 928 .86 .875 44 59 399 414 0 2003 120 1882 .813 1.23 -.299 -.299

Total number of rows: 18432

Table truncated, full table size 2149 Kbytes.




Supplementary data files not provided
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