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Sample GSM75816 Query DataSets for GSM75816
Status Public on Sep 23, 2005
Title HMEC-C Confluent.
Sample type RNA
 
Channel 1
Source name CR1 reference
Organism Homo sapiens
Characteristics CR1 reference
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name HMEC-C Confluent
Organism Homo sapiens
Characteristics HMEC-C Confluent
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-line, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2284.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 1345 1220 230 251 1115 969 279 277 65 51 .875 52 1221 .779 .911 38 46 62 70 0 1694 348 1346 1.207 .828 .272
2 1663 1512 219 241 1444 1271 278 269 86 76 .866 52 1087 .825 .917 37 45 70 78 0 2100 334 1766 1.223 .818 .29
3 1134 680 218 234 916 446 274 259 88 82 .54 52 943 .452 .783 37 45 79 87 0 944 325 619 .676 1.48 -.565
4 1253 332 210 233 1043 99 269 258 84 32 .096 52 939 .146 .423 37 45 88 96 0 461 323 138 .132 7.558 -2.918
5 3007 869 207 231 2800 638 261 252 94 82 .253 52 935 .211 .804 37 45 97 105 0 1206 320 886 .316 3.16 -1.66
6 1709 931 209 234 1500 697 254 241 86 84 .475 52 937 .435 .898 37 45 106 114 0 1293 325 968 .645 1.55 -.632
7 600 355 216 235 384 120 255 241 73 48 .327 52 957 .239 .68 36 44 115 123 0 493 326 167 .435 2.299 -1.201
8 3916 1031 213 232 3703 799 252 239 82 69 .218 52 959 .211 .972 36 44 124 132 0 1431 322 1109 .299 3.339 -1.739
9 441 305 235 234 206 71 269 241 55 30 .361 52 955 .26 .626 36 44 133 141 0 423 325 98 .476 2.102 -1.072
10 2364 1615 240 237 2124 1378 292 257 73 61 .629 52 951 .593 .944 36 44 142 150 0 2243 329 1914 .901 1.11 -.15
11 1505 2634 236 235 1269 2399 303 270 78 84 1.803 52 943 1.613 .912 36 44 151 159 0 3658 326 3332 2.626 .381 1.393
12 937 524 236 235 701 289 301 270 57 42 .462 52 959 .422 .863 35 43 160 168 0 727 326 401 .572 1.748 -.806
13 685 586 230 231 455 355 294 268 65 63 .745 52 947 .686 .871 35 43 168 176 0 813 320 493 1.084 .923 .116
14 709 469 225 227 484 242 265 250 82 63 .444 52 943 .452 .724 35 43 177 185 0 651 315 336 .694 1.44 -.527
15 5457 1403 228 227 5229 1176 262 242 75 65 .236 52 939 .218 .963 35 43 186 194 0 1948 315 1633 .312 3.202 -1.679
16 1120 470 228 228 892 242 258 236 76 59 .258 52 935 .447 .826 35 43 195 203 0 652 316 336 .377 2.655 -1.409
17 790 680 244 230 546 450 311 252 67 61 .852 52 937 .616 .82 35 43 204 212 0 944 319 625 1.145 .874 .195
18 348 290 246 234 102 56 314 257 44 9 .414 52 957 .306 .496 34 42 213 221 0 402 325 77 .755 1.325 -.406
19 2051 1934 252 237 1799 1697 319 261 84 84 .961 52 959 .885 .942 34 42 222 230 0 2686 329 2357 1.31 .763 .39
20 875 797 263 240 612 557 351 270 63 53 .683 52 955 .605 .815 34 42 231 239 0 1106 333 773 1.263 .792 .337

Total number of rows: 9216

Table truncated, full table size 1024 Kbytes.




Supplementary data files not provided
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