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Sample GSM72184 Query DataSets for GSM72184
Status Public on Aug 27, 2005
Title CLL-51
Sample type RNA
 
Channel 1
Source name Lymphopool
Organism Homo sapiens
Characteristics Lymphopool
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name CLL-51
Organism Homo sapiens
Characteristics CLL-51
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2644.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
1 239 266 201 250 38 16 222 274 22 18 1.381 177 1142 .014 .019 92 107 39 54 0 302 284 18 .474 2.111 -1.078 -1.078
2 2656 4922 198 243 2458 4679 232 313 79 80 1.887 177 906 0 0 92 107 56 71 0 5593 276 5317 2.163 .462 1.113 1.113
3 3551 19071 191 243 3360 18828 223 315 83 90 4.933 177 896 0 0 92 107 74 89 0 21671 276 21395 6.368 .157 2.671 2.671
4 4375 1775 196 243 4179 1532 249 320 83 74 .378 177 919 0 0 91 106 91 106 0 2017 276 1741 .417 2.4 -1.263 -1.263
5 8467 13791 206 245 8261 13546 340 383 85 85 1.72 177 906 0 0 91 106 109 124 0 15671 278 15393 1.863 .537 .898 .898
6 2208 3128 211 246 1997 2882 428 406 63 67 1.41 177 919 1.341 .926 90 105 126 141 0 3554 279 3275 1.64 .61 .714 .714
7 4670 2929 214 247 4456 2682 467 406 66 68 .614 177 919 0 0 90 105 144 159 0 3328 280 3048 .684 1.462 -.548 -.548
8 2406 2046 214 248 2192 1798 441 349 59 64 .802 177 928 .76 .924 89 104 162 177 0 2325 281 2044 .932 1.072 -.101 -.101
9 3221 1642 214 251 3007 1391 479 351 68 71 .469 177 906 .429 .882 89 104 179 194 0 1865 285 1580 .525 1.903 -.928 -.928
10 2111 1082 208 255 1903 827 460 428 67 61 .453 177 919 .407 .894 88 103 197 212 0 1229 289 940 .494 2.024 -1.018 -1.018
11 5002 6830 211 257 4791 6573 542 487 79 77 1.433 177 906 0 0 88 103 214 229 0 7761 292 7469 1.559 .641 .641 .641
12 4131 2817 202 245 3929 2572 397 366 63 60 .65 177 919 null null 87 102 232 247 0 3201 278 2923 .744 1.344 -.427 -.427
13 276 296 205 242 71 54 324 336 33 24 .811 177 906 .291 .376 87 102 249 264 0 336 275 61 .859 1.164 -.219 -.219
14 2568 4860 200 248 2368 4612 308 528 66 73 1.86 177 896 0 0 87 102 267 282 0 5522 281 5241 2.213 .452 1.146 1.146
15 3499 19378 209 248 3290 19130 399 508 76 83 5.683 177 930 0 0 86 101 284 299 0 22020 281 21739 6.608 .151 2.724 2.724
16 5426 2006 222 257 5204 1749 460 427 77 75 .342 177 919 0 0 86 101 302 317 0 2279 292 1987 .382 2.619 -1.389 -1.389
17 8838 13427 209 265 8629 13162 372 372 78 76 1.508 177 919 0 0 85 100 320 335 0 15257 301 14956 1.733 .577 .793 .793
18 3372 4454 207 251 3165 4203 358 340 77 84 1.366 177 906 0 0 85 100 337 352 0 5061 285 4776 1.509 .663 .594 .594
19 6298 3667 215 242 6083 3425 345 300 74 74 .568 177 919 0 0 84 99 355 370 0 4167 275 3892 .64 1.563 -.644 -.644
20 3297 2537 209 245 3088 2292 364 302 75 75 .704 177 906 .751 .93 84 99 372 387 0 2882 278 2604 .843 1.186 -.246 -.246

Total number of rows: 18432

Table truncated, full table size 2183 Kbytes.




Supplementary data files not provided
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