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Sample GSM1884 Query DataSets for GSM1884
Status Public on Jun 27, 2002
Title HMEC-C+IFNalpha
Sample type RNA
 
Channel 1
Source name CR1 reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name HMEC-C+IFNalpha 24hours
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Category: Cell-line
Subcategory: Breast
HMEC+IFNalpha 24hours done by chuck perou
Scanning Software: ScanAlyze
Software version: 2.44
Lot batch = svcc500
 
Submission date Jun 18, 2002
Last update date Nov 21, 2005
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)
GSE61 Molecular portraits of human breast tumors

Data table header descriptions
ID_REF
CH1B_MEAN mean channel 1 background
CH1B_MEDIAN median channel 1 background
CH1D_MEAN difference between CH1I_MEAN and CH1B_MEAN
CH2I_MEAN mean channel 2 signal
CH2D_MEAN difference of CH2I_MEAN and CH2B_MEAN
CH2B_MEAN mean of channel 2 background
CH2B_MEDIAN median of channel 2 background
CH2BN_MEDIAN normalized CH2B_MEDIAN
CH2DN_MEAN normalized CH2D_MEAN
CH2IN_MEAN normalized CH2I_MEAN
CORR simple correlation coefficient of channel 1 and channel 2 pixels
FLAG user defined flag (default=0)
VALUE same as UNF_VALUE but with flagged values removed
PIX_RAT2_MEDIAN
PERGTBCH1I_1SD standard deviation of fraction of pixels greater than CH1B_MEAN
PERGTBCH2I_1SD standard deviation of fraction of pixels greater than CH2B_MEAN
RAT1_MEAN ratio of CH1D_MEAN to CH2D_MEAN
RAT1N_MEAN ratio of CH1DN_MEAN to CH2DN_MEAN
RAT2_MEAN ratio of CH2D_MEAN to CH1D_MEAN
RAT2N_MEAN ratio of CH2DN_MEAN and CH1DN_MEAN
REGR slope of the simple regression line of channel 2 to channel 1 pixels
TOT_BPIX total number of background pixels
TOT_SPIX total number of signal (spot) pixels
TOP vertical, short-axis spot ellipse minimum pixel coordinate
BOT vertical, short-axis spot ellipse maximum pixel coordinate
LEFT horizontal, long-axis spot ellipse minimum pixel coordinate
RIGHT horizontal, long-axis spot ellipse maximum pixel coordinate
UNF_VALUE aka LOG_RAT2N_MEAN, or log10 of ratio of CH2DN_MEAN and CH1DN_MEAN

Data table
ID_REF CH1B_MEAN CH1B_MEDIAN CH1D_MEAN CH2I_MEAN CH2D_MEAN CH2B_MEAN CH2B_MEDIAN CH2BN_MEDIAN CH2DN_MEAN CH2IN_MEAN CORR FLAG VALUE PIX_RAT2_MEDIAN PERGTBCH1I_1SD PERGTBCH2I_1SD RAT1_MEAN RAT1N_MEAN RAT2_MEAN RAT2N_MEAN REGR TOT_BPIX TOT_SPIX TOP BOT LEFT RIGHT UNF_VALUE
1 705 626 1722 3814 2123 1737 1691 1565 1966 3531 .866 0 .191 1.148 57 42 .811 .876 1.233 1.142 1.048 1213 52 59 67 65 73 .191
2 700 623 2142 5108 3438 1721 1670 1546 3183 4729 .898 0 .571 1.418 78 67 .623 .673 1.605 1.486 1.368 1069 52 59 67 73 81 .571
3 711 632 1804 2944 1219 1765 1725 1597 1128 2725 .76 0 -.677 .683 67 57 1.48 1.599 .676 .625 .509 937 52 59 67 82 90 -.677
4 703 639 1626 1697 1765 1719 1591 1571 .114 0 .104 76 1 .043 943 52 59 67 91 99
5 685 610 6000 4337 2684 1706 1653 1530 2485 4015 .952 0 -1.272 .451 80 69 2.235 2.414 .447 .414 .416 943 52 59 67 100 108 -1.272
6 675 601 2217 3431 1846 1622 1585 1467 1709 3176 .876 0 -.375 .739 69 69 1.201 1.297 .833 .771 .705 943 52 59 67 109 117 -.375
7 643 582 643 1758 220 1575 1538 1424 203 1627 .362 0 -1.663 .302 63 13 2.923 3.167 .342 .316 .205 931 52 59 67 118 126 -1.663
8 649 598 7164 3238 1729 1547 1509 1397 1601 2998 .925 0 -2.162 .283 71 46 4.143 4.475 .241 .223 .242 931 52 59 67 127 135 -2.162
9 647 598 394 1814 294 1559 1520 1407 272 1679 .573 0 -.535 1.144 42 19 1.34 1.449 .746 .69 .593 925 52 59 67 135 143 -.535
10 634 573 3854 4073 2558 1549 1515 1402 2369 3771 .944 0 -.702 .64 61 48 1.507 1.627 .664 .615 .632 925 52 59 67 144 152 -.702
11 619 556 2008 6348 4853 1523 1495 1384 4493 5877 .892 0 1.162 2.526 78 67 .414 .447 2.417 2.238 2.229 943 52 59 67 153 161 1.162
12 627 558 1171 2223 763 1486 1460 1351 707 2058 .791 0 -.728 .777 55 38 1.535 1.656 .652 .604 .522 943 52 59 67 162 170 -.728
13 611 544 555 2094 688 1404 1406 1301 637 1938 .719 0 .199 1.408 53 30 .807 .871 1.24 1.148 .759 943 52 59 67 171 179 .199
14 596 537 722 1790 438 1357 1352 1251 406 1657 .507 0 -.831 .562 67 19 1.648 1.778 .607 .562 .488 939 52 59 67 180 188 -.831
15 602 544 10883 4067 2720 1351 1347 1247 2518 3765 .94 0 -2.112 .282 69 48 4.001 4.322 .25 .231 .239 931 52 59 67 189 197 -2.112
16 602 538 1137 1713 360 1352 1353 1252 334 1586 .464 0 -1.767 .276 71 15 3.158 3.404 .317 .294 .242 931 52 59 67 198 206 -1.767
17 608 524 973 2447 1067 1383 1380 1277 988 2265 .71 0 .022 1.087 67 44 .912 .985 1.097 1.015 .778 925 52 59 67 206 214 .022
18 620 529 235 1398 10 1401 1388 1285 9 1294 .078 0 -4.707 .782 42 3 23.5 26.111 .043 .038 .066 935 52 59 67 215 223 -4.707
19 618 525 3139 4721 3332 1403 1389 1286 3085 4371 .929 0 -.025 .915 76 59 .942 1.018 1.061 .983 .98 951 52 59 67 224 232 -.025
20 608 512 1310 2841 1461 1405 1380 1277 1353 2630 .826 0 .047 .869 63 44 .897 .968 1.115 1.033 .901 955 52 59 67 233 241 .047

Total number of rows: 9216

Table truncated, full table size 1165 Kbytes.




Supplementary data files not provided
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