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Sample GSM72136 Query DataSets for GSM72136
Status Public on Aug 27, 2005
Title CLL-68
Sample type RNA
 
Channel 1
Source name Lymphopool
Organism Homo sapiens
Characteristics Lymphopool
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name CLL-68
Organism Homo sapiens
Characteristics CLL-68
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2665.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
1 221 393 191 385 30 8 205 399 23 11 1.048 177 1142 .283 .216 75 90 69 84 0 644 631 13 .433 2.308 -1.206 -1.206
2 2439 2981 194 378 2245 2603 207 408 62 60 1.188 177 896 0 0 75 90 87 102 0 4886 619 4267 1.901 .526 .927 .927
3 3644 15910 201 375 3443 15535 216 411 77 80 4.041 177 883 0 0 75 90 104 119 0 26081 614 25467 7.397 .135 2.887 2.887
4 3933 1173 204 397 3729 776 220 421 66 42 .234 177 896 .974 2 75 90 121 136 0 1922 650 1272 .341 2.932 -1.552 -1.552
5 7059 6910 216 411 6843 6499 233 427 78 71 .988 177 886 0 0 75 90 139 154 0 11327 673 10654 1.557 .642 .639 .639
6 1909 1913 223 430 1686 1483 242 445 51 42 .944 177 896 .823 .953 75 90 156 171 0 3136 704 2432 1.442 .693 .529 .529
7 5156 2609 213 443 4943 2166 232 452 72 50 .458 177 896 0 0 75 90 174 189 0 4277 726 3551 .718 1.392 -.477 -.477
8 2643 1642 207 436 2436 1206 222 453 70 57 .521 177 896 .505 .931 75 90 191 206 0 2691 714 1977 .812 1.232 -.301 -.301
9 2927 1192 209 444 2718 748 222 461 69 47 .303 177 896 .256 .924 75 90 209 224 0 1954 727 1227 .451 2.215 -1.147 -1.147
10 2259 1023 214 475 2045 548 235 487 64 44 .311 177 896 .254 .903 75 90 226 241 0 1677 778 899 .44 2.275 -1.186 -1.186
11 5512 5792 215 480 5297 5312 246 494 74 66 1.011 177 896 0 0 75 90 244 259 0 9495 786 8709 1.644 .608 .717 .717
12 4919 3342 222 469 4697 2873 246 487 72 67 .633 177 896 0 0 75 90 261 276 0 5478 768 4710 1.003 .997 .004 .004
13 363 612 221 465 142 147 252 482 31 25 1.251 177 896 1.082 .768 75 90 279 294 0 1003 762 241 1.697 .589 .763 .763
14 2860 4094 213 465 2647 3629 256 619 68 69 1.316 177 883 null null 75 90 296 311 0 6711 762 5949 2.247 .445 1.168 1.168
15 3401 15849 218 465 3183 15384 267 649 74 78 4.306 177 896 0 0 75 90 313 328 0 25981 762 25219 7.923 .126 2.986 2.986
16 4619 1403 225 446 4394 957 282 620 72 61 .226 177 886 0 0 75 90 331 346 0 2300 731 1569 .357 2.801 -1.486 -1.486
17 11172 12399 221 448 10951 11951 265 479 79 76 1.115 177 905 0 0 75 90 348 363 0 20326 734 19592 1.789 .559 .839 .839
18 2769 2726 220 447 2549 2279 264 472 68 71 .874 177 919 .846 .93 75 90 366 381 0 4468 732 3736 1.466 .682 .552 .552
19 5961 3224 219 438 5742 2786 268 453 75 71 .494 177 928 0 0 75 90 383 398 0 5285 718 4567 .795 1.257 -.33 -.33
20 3004 2457 223 450 2781 2007 276 471 70 66 .73 177 928 .675 .884 75 90 401 416 0 4027 737 3290 1.183 .845 .242 .242

Total number of rows: 18432

Table truncated, full table size 2170 Kbytes.




Supplementary data files not provided
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