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Sample GSM72199 Query DataSets for GSM72199
Status Public on Aug 27, 2005
Title CLL-70;Lymph node
Sample type RNA
 
Channel 1
Source name Lymphopool
Organism Homo sapiens
Characteristics Lymphopool
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name CLL-70;Lymph node
Organism Homo sapiens
Characteristics CLL-70;Lymph node
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Chronic Lymphocytic Leukemia, Untreated watch&wait patients
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2617.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
1 899 2433 321 244 578 2189 359 260 40 56 2.392 225 1041 3.551 1.703 55 72 93 110 0 1634 164 1470 2.544 .393 1.347 1.347
2 1924 4478 318 219 1606 4259 341 233 57 58 2.461 225 745 0 0 55 72 111 128 0 3008 147 2861 1.781 .561 .833 .833
3 2178 16674 296 209 1882 16465 326 220 56 75 7.877 225 731 0 0 55 72 128 145 0 11200 140 11059 5.876 .17 2.555 2.555
4 3187 2538 283 204 2904 2334 313 213 59 52 .74 225 720 0 0 55 72 146 163 0 1705 137 1568 .54 1.852 -.889 -.889
5 2104 10278 270 195 1834 10083 299 202 57 64 4.727 225 720 0 0 55 72 163 180 0 6903 131 6773 3.693 .271 1.885 1.885
6 1731 4052 275 197 1456 3855 304 204 57 57 2.365 225 731 0 0 55 72 181 198 0 2722 132 2589 1.778 .562 .831 .831
7 3529 6508 271 209 3258 6299 306 213 68 59 1.694 225 720 0 0 55 72 198 215 0 4371 140 4231 1.299 .77 .377 .377
8 1977 3267 287 227 1690 3040 322 237 56 48 1.603 225 771 0 0 54 71 216 233 0 2194 152 2042 1.208 .828 .273 .273
9 2346 4354 313 242 2033 4112 343 265 57 61 1.902 225 756 0 0 54 71 234 251 0 2924 163 2762 1.359 .736 .442 .442
10 1937 2337 322 242 1615 2095 360 282 56 60 1.063 225 756 1.222 .785 54 71 251 268 0 1570 163 1407 .871 1.148 -.199 -.199
11 2477 5178 318 237 2159 4941 354 263 60 64 2.032 225 745 0 0 54 71 269 286 0 3478 159 3319 1.537 .651 .62 .62
12 2813 4561 299 212 2514 4349 322 223 55 55 1.575 225 731 0 0 54 71 286 303 0 3064 142 2921 1.162 .861 .217 .217
13 526 709 272 205 254 504 302 209 47 39 1.178 225 731 1.6 .781 54 71 304 321 0 476 138 339 1.333 .75 .414 .414
14 1756 3680 269 205 1487 3475 299 207 59 50 2.169 225 720 2.165 2.891 54 71 321 338 0 2472 138 2334 1.57 .637 .65 .65
15 2116 14283 253 204 1863 14079 293 206 60 65 6.46 225 735 0 0 54 71 339 356 0 9594 137 9457 5.076 .197 2.344 2.344
16 3339 2417 261 203 3078 2214 298 209 62 54 .685 225 756 0 0 53 70 357 374 0 1623 136 1487 .483 2.07 -1.049 -1.049
17 2067 9383 268 206 1799 9177 304 212 60 62 4.498 225 756 0 0 53 70 374 391 0 6302 138 6164 3.426 .292 1.777 1.777
18 1646 3235 268 211 1378 3024 313 216 63 56 2.025 225 756 0 0 53 70 392 409 0 2173 142 2031 1.474 .678 .56 .56
19 3468 5169 302 219 3166 4950 360 246 63 60 1.47 225 746 0 0 53 70 409 426 0 3472 147 3325 1.05 .952 .071 .071
20 1828 3081 307 233 1521 2848 361 258 60 62 1.645 225 741 0 0 53 70 427 444 0 2069 157 1913 1.258 .795 .331 .331

Total number of rows: 18432

Table truncated, full table size 2173 Kbytes.




Supplementary data files not provided
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