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Sample GSM72218 Query DataSets for GSM72218
Status Public on Aug 27, 2005
Title CLL-15
Sample type RNA
 
Channel 1
Source name Lymphopool
Organism Homo sapiens
Characteristics Lymphopool
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name CLL-15
Organism Homo sapiens
Characteristics CLL-15
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Chronic Lymphocytic Leukemia, Fludarabine chemotherapy
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2985.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
1 570 461 470 249 100 212 502 259 25 27 .824 208 1050 .956 .684 85 101 70 86 0 317 171 146 1.46 .685 .546 .546
2 1227 1668 443 249 784 1419 467 260 51 60 1.801 208 777 .774 .759 85 101 88 104 0 1148 171 977 1.246 .802 .318 .318
3 1288 2739 440 240 848 2499 467 253 59 59 2.731 208 765 2.569 .903 85 101 105 121 0 1886 165 1721 2.029 .493 1.021 1.021
4 1281 491 433 233 848 258 464 248 50 47 .307 208 781 .268 .814 85 101 123 139 0 338 160 178 .209 4.774 -2.255 -2.255
5 1177 1847 419 230 758 1617 484 321 53 56 1.904 208 768 1.821 .887 85 101 141 157 0 1272 158 1113 1.469 .681 .555 .555
6 927 1016 416 224 511 792 479 311 59 56 1.475 208 765 1.188 .794 85 101 158 174 0 700 154 545 1.067 .937 .094 .094
7 1584 1533 429 234 1155 1299 459 244 52 58 1.175 208 802 .975 .921 84 100 176 192 0 1056 161 894 .774 1.291 -.369 -.369
8 929 725 411 229 518 496 454 242 53 52 .892 208 799 .759 .841 84 100 193 209 0 499 158 342 .659 1.517 -.601 -.601
9 1030 603 401 225 629 378 445 235 55 48 .594 208 802 .51 .872 84 100 211 227 0 415 155 260 .414 2.417 -1.273 -1.273
10 890 467 398 232 492 235 479 292 50 47 .493 208 789 .395 .843 84 100 228 244 0 322 160 162 .329 3.041 -1.604 -1.604
11 1275 1599 392 235 883 1364 475 296 60 58 1.541 208 777 1.376 .897 84 100 246 262 0 1101 162 939 1.064 .94 .089 .089
12 1318 1167 408 241 910 926 447 250 53 49 .962 208 765 .937 .91 84 100 263 279 0 804 166 638 .701 1.427 -.513 -.513
13 579 382 410 240 169 142 472 305 30 25 .541 208 768 .57 .643 84 100 281 297 0 263 165 98 .579 1.729 -.79 -.79
14 874 1145 398 233 476 912 464 300 52 53 1.552 208 765 1.358 .552 84 100 298 314 0 788 160 628 1.319 .758 .4 .4
15 1165 2488 397 235 768 2253 461 261 57 61 2.883 208 802 2.325 .894 83 99 316 332 0 1713 162 1551 2.02 .495 1.014 1.014
16 1316 567 404 235 912 332 458 242 58 50 .367 208 799 .342 .855 83 99 333 349 0 390 162 229 .251 3.99 -1.996 -1.996
17 1588 2821 388 235 1200 2586 461 241 52 52 1.967 208 802 0 0 83 99 351 367 0 1942 162 1781 1.484 .674 .569 .569
18 860 1297 344 254 516 1043 396 263 47 50 1.721 208 789 1.639 .879 83 99 368 384 0 893 175 718 1.392 .719 .477 .477
19 2149 2666 282 266 1867 2400 296 278 62 60 1.245 208 777 1.228 .943 83 99 386 402 0 1836 183 1652 .885 1.13 -.176 -.176
20 1192 1517 275 270 917 1247 287 283 55 55 1.047 208 765 .754 .515 83 99 403 419 0 1045 186 859 .936 1.068 -.095 -.095

Total number of rows: 18432

Table truncated, full table size 2173 Kbytes.




Supplementary data files not provided
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