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Sample GSM97264 Query DataSets for GSM97264
Status Public on Feb 25, 2006
Title BC205B-AF
Sample type RNA
 
Channel 1
Source name CRB1 reference
Organism Homo sapiens
Characteristics CRB1 reference
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name BC205B-AF
Organism Homo sapiens
Characteristics BC205B-AF
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2000-03/3168.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 Feb 17, 2006
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 GPL2776
Series (2)
GSE3193 Breast Tumor Clinical Implications
GSE4268 Breast and ovarian 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 same as UNF_VALUE but with flagged values removed
UNF_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 UNF_VALUE
1 542 512 128 145 414 367 148 153 50 47 .77 225 990 .546 .618 201 218 192 209 0 730 207 523 1.263 .792 .337 .337
2 400 360 127 144 273 216 149 154 51 45 .745 225 756 .523 .649 200 217 209 226 0 513 205 308 1.127 .887 .173 .173
3 270 198 118 141 152 57 137 148 50 32 .513 225 756 .195 .376 200 217 227 244 0 282 201 81 .534 1.871 -.904 -.904
4 398 238 109 130 289 108 132 140 54 38 .459 225 756 .234 .519 200 217 244 261 0 339 185 154 .532 1.878 -.909 -.909
5 480 179 114 128 366 51 132 140 51 35 .228 225 756 .057 .3 200 217 262 279 0 255 182 73 .199 5.036 -2.332 -2.332
6 652 353 114 131 538 222 132 141 54 43 .432 225 756 .259 .575 200 217 279 296 0 503 187 316 .588 1.701 -.766 -.766
7 196 188 119 133 77 55 135 141 39 38 .642 225 756 .134 .191 200 217 297 314 0 268 190 78 1.018 .983 .025 .025
8 1621 387 125 127 1496 260 143 136 54 40 .205 225 756 .116 .632 200 217 314 331 0 551 181 370 .248 4.038 -2.014 -2.014
9 280 167 124 133 156 34 143 142 48 31 .407 225 756 .078 .211 200 217 332 349 0 238 190 48 .311 3.22 -1.687 -1.687
10 1766 1277 124 144 1642 1133 145 154 55 48 .673 225 756 .466 .68 200 217 349 366 0 1820 205 1614 .983 1.017 -.024 -.024
11 601 605 127 159 474 446 322 179 53 43 1.069 225 745 .089 .289 200 217 367 384 0 862 227 636 1.341 .746 .423 .423
12 361 311 131 164 230 147 327 183 43 42 .665 225 731 .044 .404 200 217 384 401 0 443 234 209 .911 1.098 -.135 -.135
13 227 229 127 161 100 68 145 172 44 38 .692 225 720 .17 .267 200 217 402 419 0 326 229 97 .969 1.032 -.046 -.046
14 388 539 125 172 263 367 142 181 48 47 1.278 225 720 .907 .661 200 217 419 436 0 768 245 523 1.988 .503 .992 .992
15 2267 1337 127 184 2140 1153 142 194 57 48 .641 225 720 .399 .724 200 217 437 454 0 1905 262 1643 .768 1.303 -.381 -.381
16 525 289 149 151 376 138 168 165 52 56 .391 225 720 .182 .57 200 217 454 471 0 412 215 197 .523 1.912 -.935 -.935
17 497 239 170 110 327 129 199 127 40 30 .388 225 720 .177 .352 200 217 472 489 0 341 157 184 .562 1.779 -.831 -.831
18 1476 191 149 103 1327 88 175 116 56 48 .149 225 720 .039 .539 200 217 489 506 0 272 147 125 .094 10.583 -3.404 -3.404
19 1093 568 104 110 989 458 132 123 62 51 .459 225 720 .339 .681 200 217 507 524 0 809 157 653 .66 1.515 -.6 -.6
20 556 284 109 121 447 163 133 130 52 39 .358 225 720 .225 .585 200 217 524 541 0 405 172 232 .52 1.925 -.945 -.945

Total number of rows: 9216

Table truncated, full table size 1076 Kbytes.




Supplementary data files not provided
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