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Sample GSM94477 Query DataSets for GSM94477
Status Public on Feb 01, 2006
Title SKN005 Normal Kidney
Sample type RNA
 
Channel 1
Source name crc
Organism Homo sapiens
Characteristics crc
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name SKN005
Organism Homo sapiens
Characteristics SKN005
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Kidney, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2373.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 Jan 30, 2006
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 GPL2649
Series (1)
GSE4125 Renal Cell Carcinoma

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 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
1 390 473 354 461 36 12 400 488 13 5 1.065 80 1361 .209 .253 94 104 113 123 0 622 606 16 .444 2.25 -1.17
2 352 470 380 467 null 3 424 496 2 5 .66 80 1201 .203 .236 94 104 128 138 0 618 614 4 null null null
3 380 486 400 486 null null 660 760 2 2 1.537 80 1201 .695 .779 93 103 143 153 0 639 639 null null null null
4 2585 3247 432 518 2153 2729 1304 942 92 88 1.46 80 1201 .47 .557 93 103 158 168 -100 4272 681 3591 1.668 .6 .738
5 4980 691 464 520 4516 171 1384 901 95 31 .048 80 1201 .066 .253 93 103 173 183 -100 909 684 225 .05 20.071 -4.327
6 492 535 494 520 null 15 1140 829 3 5 1.174 80 1201 .38 .612 93 103 188 198 0 703 684 19 null null null
7 3694 3988 546 560 3148 3428 904 1044 78 81 1.052 80 1188 .902 .845 93 103 203 213 0 5247 736 4511 1.433 .698 .519
8 3055 7336 569 575 2486 6761 1012 1112 80 97 3.076 97 1171 1.802 .809 93 104 217 228 -100 9652 756 8896 3.578 .279 1.839
9 8457 2579 538 541 7919 2038 1150 1022 98 82 .246 97 1175 .217 .624 93 104 232 243 -100 3393 711 2682 .339 2.953 -1.562
10 724 608 385 453 339 155 932 725 35 22 .622 80 1144 .318 .467 93 103 249 259 0 800 596 204 .602 1.662 -.733
11 1832 2104 321 402 1511 1702 422 460 89 85 1.219 137 1087 .98 .871 91 104 263 276 0 2768 528 2240 1.482 .675 .568
12 5511 2558 321 407 5190 2151 379 454 99 94 .432 137 1095 .35 .891 91 104 276 289 0 3365 535 2830 .545 1.834 -.875
13 596 470 316 389 280 81 449 439 45 22 .587 80 1169 .157 .52 94 104 294 304 0 618 511 107 .382 2.617 -1.388
14 15215 3132 306 390 14909 2742 430 461 92 86 .175 80 1201 .149 .839 92 102 309 319 0 4121 513 3608 .242 4.132 -2.047
15 923 9119 300 393 623 8726 366 442 81 95 13.77 80 1201 3.891 .501 92 102 324 334 0 11998 517 11481 18.429 .054 4.204
16 1374 446 329 420 1045 26 378 455 82 15 .082 80 1184 .03 .121 92 102 339 349 0 586 552 34 .033 30.735 -4.942
17 14600 3344 351 450 14249 2894 401 473 81 85 .206 97 1192 .169 .851 92 103 352 363 0 4400 592 3808 .267 3.742 -1.904
18 745 799 381 491 364 308 436 521 77 66 .796 80 1139 .198 .408 91 101 369 379 0 1051 646 405 1.113 .899 .154
19 2176 2922 366 466 1810 2456 398 494 90 94 1.344 137 1148 1.158 .92 90 103 381 394 0 3844 613 3231 1.785 .56 .836
20 1830 1983 333 408 1497 1575 368 446 92 95 1.037 80 1101 .844 .838 91 101 397 407 0 2609 536 2073 1.385 .722 .47

Total number of rows: 24192

Table truncated, full table size 2724 Kbytes.




Supplementary data files not provided
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