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Sample GSM1890 Query DataSets for GSM1890
Status Public on Jun 27, 2002
Title BC115A-AF
Sample type RNA
 
Channel 1
Source name CR1 reference
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name BC115A-AF
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Category: Primary tumor
Subcategory: Breast
Scanning Software: ScanAlyze
Software version: 2.44
Lot batch = svcc64
 
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 (3)
GSE61 Molecular portraits of human breast tumors
GSE4336 Breast tumors
GSE4382 Repeated observation of breast tumor subtypes in independent gene expression data sets

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 1084 924 652 3227 1018 2332 2209 2769 1276 4045 .926 0 .969 1.286 42 36 .64 .511 1.561 1.957 .978 1237 52 67 75 87 95 .969
2 925 863 636 2429 295 2146 2134 2675 370 3045 .566 0 -.782 .517 50 11 2.156 1.72 .464 .581 .528 1085 52 67 75 96 104 -.782
3 863 820 607 1788 2039 2042 2560 -318 2241 0 .185 51 1 951 52 67 75 105 113
4 827 762 762 1934 1963 1934 2424 0 2424 .14 0 .223 55 3 0 .063 953 52 67 75 114 122
5 778 729 3953 2050 234 1844 1816 2276 293 2570 .525 0 -3.752 .083 63 9 16.893 13.477 .059 .074 .071 955 52 67 75 123 131 -3.752
6 753 697 1453 2656 861 1798 1795 2250 1079 3329 .82 0 -.429 .589 67 48 1.688 1.346 .593 .743 .585 951 52 67 75 132 140 -.429
7 844 690 170 1508 1845 1745 2187 -297 1890 .862 0 .133 28 0 .85 947 52 67 75 141 149
8 842 689 4089 3530 1828 1814 1702 2133 2291 4425 .893 0 -.836 .49 59 42 2.237 1.785 .447 .56 .443 943 52 67 75 150 158 -.836
9 861 701 1721 1844 1744 2186 -29 2157 .882 0 1.177 13 3 0 .873 931 52 67 75 159 167
10 852 700 1999 2933 1188 1847 1745 2187 1489 3676 .897 0 -.425 .551 53 42 1.683 1.342 .594 .745 .665 951 52 66 74 168 176 -.425
11 847 696 1370 2069 360 1814 1709 2142 451 2593 .803 0 -1.602 .25 59 21 3.806 3.036 .263 .329 .622 941 52 66 74 176 184 -1.602
12 723 684 569 1722 16 1712 1706 2138 20 2158 0 -4.826 .503 44 1 35.563 28.371 .028 .035 937 52 66 74 185 193 -4.826
13 699 654 245 1506 1671 1666 2088 -201 1888 .248 0 .508 36 1 .194 941 52 66 74 193 201
14 669 630 256 1753 112 1648 1641 2057 140 2197 .146 0 -.867 .546 46 9 2.286 1.824 .438 .548 .148 937 52 66 74 202 210 -.867
15 650 606 5694 2743 1124 1626 1619 2029 1409 3438 .944 0 -2.015 .214 65 36 5.066 4.041 .197 .247 .19 939 52 66 74 211 219 -2.015
16 617 582 682 1371 1576 1578 1978 -259 1718 0 .375 61 1 941 52 66 74 220 228
17 631 599 351 1827 285 1550 1542 1933 357 2290 .601 0 .025 .574 44 13 1.232 .983 .812 1.018 .524 943 52 66 74 229 237 .025
18 623 590 35 1327 1540 1530 1918 -254 1663 .268 0 .523 21 1 .294 943 52 66 74 238 246
19 631 592 2091 3614 2098 1519 1516 1900 2630 4530 .899 0 .331 .898 61 53 .997 .795 1.003 1.258 .819 963 52 65 73 247 255 .331
20 632 592 341 1621 102 1528 1519 1904 128 2032 .435 0 -1.415 .408 42 9 3.343 2.667 .299 .375 .377 963 52 65 73 256 264 -1.415

Total number of rows: 9216

Table truncated, full table size 1126 Kbytes.




Supplementary data files not provided
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