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Sample GSM75820 Query DataSets for GSM75820
Status Public on Sep 23, 2005
Title SK-BR-3.
Sample type RNA
 
Channel 1
Source name CR2 reference
Organism Homo sapiens
Characteristics CR2 reference
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name SK-BR-3
Organism Homo sapiens
Characteristics SK-BR-3
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-line, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2210.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 Sep 22, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
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 GPL180
Series (1)
GSE3353 A comparison of gene expression signatures from breast tumors and breast tissue derived cell lines

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 LOG_RAT2N_MEDIANs 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 LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized LOG_RAT2N_MEDIAN 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 1450 3827 184 577 1266 3250 365 694 71 63 2.538 52 1213 1.92 .828 115 123 108 116 0 1760 265 1495 1.181 .847 .24
2 1679 3892 200 574 1479 3318 368 705 82 76 2.409 52 1069 1.616 .78 115 123 116 124 0 1790 264 1526 1.032 .969 .045
3 1112 2246 199 582 913 1664 372 752 69 73 1.974 52 937 1.205 .684 115 123 125 133 0 1033 268 765 .838 1.193 -.255
4 1741 687 195 587 1546 100 359 742 88 19 .131 52 943 .151 .205 115 123 134 142 0 316 270 46 .03 33.616 -5.071
5 3945 7645 191 562 3754 7083 357 674 88 84 1.707 52 943 1.733 .898 115 123 143 151 0 3516 258 3257 .868 1.152 -.205
6 2698 3685 189 560 2509 3125 365 666 82 76 1.351 52 943 1.106 .838 115 123 152 160 0 1695 258 1437 .573 1.746 -.804
7 767 1659 189 575 578 1084 363 648 67 63 1.462 52 931 .843 .541 115 123 161 169 0 763 264 499 .863 1.159 -.213
8 5457 9806 188 574 5269 9232 350 586 69 73 1.652 52 931 1.65 .94 115 123 170 178 0 4510 264 4246 .806 1.241 -.311
9 425 1066 201 586 224 480 368 605 38 40 1.638 52 925 .766 .633 115 123 178 186 0 490 270 221 .986 1.015 -.021
10 2766 6436 200 612 2566 5824 361 633 71 78 2.282 52 929 1.76 .867 115 123 187 195 0 2960 281 2678 1.044 .958 .062
11 2367 3879 202 626 2165 3253 351 649 80 65 1.563 52 951 1.423 .876 115 123 196 204 0 1784 288 1496 .691 1.447 -.533
12 1640 3123 206 633 1434 2490 353 660 71 71 1.817 52 955 1.398 .862 115 123 205 213 0 1436 291 1145 .799 1.252 -.324
13 981 1574 219 634 762 940 360 667 69 48 1.552 52 959 .889 .724 115 123 214 222 0 724 292 432 .567 1.763 -.818
14 1322 1082 206 642 1116 440 354 675 75 44 .521 52 959 .258 .564 115 123 223 231 0 498 295 202 .181 5.515 -2.463
15 6363 14344 239 641 6124 13703 364 693 82 80 2.207 52 951 2.067 .945 115 123 232 240 0 6597 295 6302 1.029 .972 .041
16 1655 1247 214 637 1441 610 359 704 75 48 .507 52 951 .38 .576 115 123 241 249 0 573 293 281 .195 5.137 -2.361
17 1140 812 219 648 921 164 373 713 69 21 .265 52 945 .181 .284 115 123 249 257 0 373 298 75 .082 12.211 -3.61
18 458 741 220 660 238 81 373 724 42 13 .444 52 951 .21 .144 115 123 258 266 0 341 304 37 .157 6.389 -2.676
19 3018 9395 215 665 2803 8730 372 723 73 80 3.051 52 963 2.751 .903 115 123 267 275 0 4321 306 4015 1.432 .698 .518
20 1059 1569 212 672 847 897 374 691 73 48 1.226 52 963 .867 .7 115 123 276 284 0 722 309 413 .487 2.053 -1.038

Total number of rows: 9216

Table truncated, full table size 1047 Kbytes.




Supplementary data files not provided
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