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Sample GSM72181 Query DataSets for GSM72181
Status Public on Aug 27, 2005
Title CLL-48
Sample type RNA
 
Channel 1
Source name Lymphopool
Organism Homo sapiens
Characteristics Lymphopool
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name CLL-48
Organism Homo sapiens
Characteristics CLL-48
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2640.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
1 300 229 235 214 65 15 261 230 28 22 .729 177 1155 .118 .153 88 103 45 60 0 602 563 39 .6 1.667 -.737 -.737
2 1688 1178 229 212 1459 966 265 244 79 70 .643 177 906 .617 .89 88 103 63 78 0 3100 557 2543 1.743 .574 .802 .802
3 3128 6660 241 213 2887 6447 284 248 92 95 2.113 177 928 0 0 87 102 80 95 0 17526 560 16966 5.877 .17 2.555 2.555
4 4237 710 261 238 3976 472 589 415 78 70 .131 177 932 0 0 87 102 98 113 0 1868 626 1242 .312 3.201 -1.679 -1.679
5 7197 6432 262 245 6935 6187 715 510 77 80 .824 177 915 0 0 87 102 116 131 -100 16926 644 16282 2.348 .426 1.231
6 2280 1349 241 218 2039 1131 583 611 80 76 .551 177 896 .493 .816 87 102 133 148 0 3550 573 2977 1.46 .685 .546 .546
7 4775 1715 225 197 4550 1518 375 468 81 80 .329 177 919 0 0 86 101 151 166 0 4513 518 3995 .878 1.139 -.188 -.188
8 2478 1128 225 197 2253 931 350 239 84 82 .375 177 906 .336 .789 86 101 168 183 0 2968 518 2450 1.087 .92 .121 .121
9 3097 953 221 196 2876 757 349 232 74 72 .272 177 896 .233 .829 86 101 186 201 0 2507 515 1992 .693 1.444 -.53 -.53
10 2438 613 223 195 2215 418 470 282 80 73 .19 177 919 .165 .756 85 100 203 218 0 1613 513 1100 .497 2.014 -1.01 -1.01
11 4690 2634 229 202 4461 2432 510 301 73 72 .567 177 906 0 0 85 100 221 236 0 6931 531 6400 1.435 .697 .521 .521
12 4112 1610 220 207 3892 1403 317 247 81 74 .39 177 896 0 0 85 100 238 253 0 4236 544 3692 .949 1.054 -.076 -.076
13 281 234 227 225 54 9 331 265 23 19 1.123 177 919 .127 .207 84 99 256 271 0 615 592 23 .426 2.348 -1.231 -1.231
14 2492 1732 233 229 2259 1503 324 271 72 74 .66 177 880 .577 .875 84 99 273 288 0 4557 602 3955 1.751 .571 .808 .808
15 4329 9710 223 234 4106 9476 400 282 94 96 2.147 177 1056 0 0 80 95 289 304 0 25552 615 24937 6.073 .165 2.602 2.602
16 5241 869 228 235 5013 634 610 351 74 67 .134 177 948 0 0 83 98 309 324 0 2286 618 1668 .333 3.005 -1.588 -1.588
17 10489 7892 227 226 10262 7666 559 330 80 83 .725 177 906 0 0 83 98 326 341 0 20768 594 20174 1.966 .509 .975 .975
18 3169 1624 234 228 2935 1396 431 309 81 80 .453 177 906 .458 .87 83 98 344 359 0 4273 600 3673 1.251 .799 .324 .324
19 6170 2046 235 230 5935 1816 437 270 75 75 .304 177 919 0 0 82 97 361 376 0 5384 605 4779 .805 1.242 -.313 -.313
20 2944 1262 225 209 2719 1053 393 249 75 80 .386 177 906 .374 .859 82 97 379 394 0 3321 550 2771 1.019 .981 .027 .027

Total number of rows: 18432

Table truncated, full table size 2169 Kbytes.




Supplementary data files not provided
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