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Sample GSM72192 Query DataSets for GSM72192
Status Public on Aug 27, 2005
Title CLL-39
Sample type RNA
 
Channel 1
Source name Lymphopool
Organism Homo sapiens
Characteristics Lymphopool
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name CLL-39
Organism Homo sapiens
Characteristics CLL-39
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Chronic Lymphocytic Leukemia, Fludarabine chemotherapy
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2975.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
1 281 641 221 474 60 167 236 501 33 28 1.802 156 1186 .521 .259 84 98 124 138 0 668 494 174 2.9 .345 1.536 1.536
2 1119 2775 220 489 899 2286 253 636 70 70 2.475 156 966 2.282 .895 84 98 142 156 0 2891 509 2382 2.649 .377 1.406 1.406
3 1541 12807 226 489 1315 12318 259 658 71 78 9.02 156 955 0 0 84 98 159 173 0 13343 509 12834 9.759 .102 3.287 3.287
4 1863 2114 212 489 1651 1625 240 554 67 58 .931 156 958 .942 .948 84 98 177 191 0 2203 509 1693 1.025 .975 .036 .036
5 3959 10577 196 468 3763 10109 221 498 75 74 2.39 156 943 0 0 84 98 194 208 0 11020 488 10532 2.799 .357 1.485 1.485
6 1813 5121 196 460 1617 4661 233 494 71 64 2.566 156 985 0 0 83 97 211 225 0 5335 479 4856 3.003 .333 1.586 1.586
7 6008 4842 202 468 5806 4374 240 502 85 76 .738 156 987 0 0 83 97 229 243 0 5045 488 4557 .785 1.274 -.349 -.349
8 1840 2706 212 475 1628 2231 238 496 68 60 1.264 156 976 1.278 .934 83 97 246 260 0 2819 495 2324 1.428 .7 .514 .514
9 2421 1932 221 477 2200 1455 245 490 68 57 .662 156 956 .61 .945 83 97 264 278 0 2013 497 1516 .689 1.451 -.537 -.537
10 1753 1570 234 488 1519 1082 268 514 64 49 .774 156 955 .65 .91 83 97 281 295 0 1636 508 1127 .742 1.347 -.43 -.43
11 3170 5653 264 530 2906 5123 301 560 77 72 1.64 156 958 0 0 83 97 299 313 0 5890 552 5337 1.837 .544 .877 .877
12 3481 4893 275 535 3206 4358 303 565 73 64 1.265 156 985 0 0 82 96 316 330 0 5098 557 4540 1.416 .706 .502 .502
13 414 796 254 508 160 288 278 531 28 26 1.708 156 988 1.14 .8 82 96 334 348 0 829 529 300 1.875 .533 .907 .907
14 2162 5424 221 489 1941 4935 252 587 65 63 2.409 156 964 0 0 82 96 351 365 0 5651 509 5142 2.649 .378 1.405 1.405
15 1891 14905 206 485 1685 14420 241 613 73 76 8.23 156 964 0 0 82 96 368 382 0 15529 505 15024 8.916 .112 3.156 3.156
16 1867 1896 200 460 1667 1436 218 569 66 53 .846 156 957 .82 .925 82 96 386 400 0 1975 479 1496 .897 1.114 -.156 -.156
17 3875 8466 186 452 3689 8014 199 471 75 67 2.024 156 955 0 0 82 96 403 417 0 8820 471 8350 2.263 .442 1.178 1.178
18 1732 4464 185 464 1547 4000 201 477 66 68 2.49 156 987 0 0 81 95 421 435 0 4651 483 4167 2.694 .371 1.43 1.43
19 5527 4279 185 463 5342 3816 200 475 73 62 .665 156 985 0 0 81 95 438 452 0 4458 482 3976 .744 1.344 -.426 -.426
20 2127 2627 190 448 1937 2179 206 467 64 57 1.08 156 968 1.066 .941 81 95 456 470 0 2737 467 2270 1.172 .853 .229 .229

Total number of rows: 18432

Table truncated, full table size 2177 Kbytes.




Supplementary data files not provided
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