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Sample GSM96021 Query DataSets for GSM96021
Status Public on Feb 25, 2006
Title Ovarian Ca OV407
Sample type RNA
 
Channel 1
Source name CRD Reference
Organism Homo sapiens
Characteristics CRD Reference
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Ovarian Ca OV407
Organism Homo sapiens
Characteristics Ovarian Ca OV407
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Solid tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11736.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 07, 2006
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
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 GPL178
Series (2)
GSE4198 Ovarian cancers
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
1 310 531 57 152 253 379 61 176 64 62 1.412 112 1233 1.338 .719 74 86 79 91 -100 931 266 665 2.628 .38 1.394
2 291 502 64 151 227 351 68 175 69 66 1.7 112 1009 1.266 .701 74 86 93 105 -100 880 264 616 2.714 .369 1.44
3 306 537 72 151 234 386 74 168 75 76 1.403 112 1017 1.158 .564 74 86 108 120 -100 942 264 678 2.897 .345 1.535
4 287 602 76 152 211 450 77 160 81 82 2.126 112 1017 1.699 .751 74 86 123 135 -100 1056 266 790 3.744 .267 1.905
5 685 682 82 153 603 529 85 165 88 83 .902 112 1017 .788 .822 74 86 138 150 0 1196 268 928 1.539 .65 .622 .622
6 423 820 91 158 332 662 93 172 89 87 1.676 112 1017 1.621 .777 74 86 153 165 -100 1438 277 1161 3.497 .286 1.806
7 221 418 88 163 133 255 90 174 53 58 1.749 112 1017 1.271 .622 74 86 168 180 -100 733 285 448 3.368 .297 1.752
8 207 454 85 161 122 293 87 174 60 66 2.274 112 1017 1.347 .545 74 86 183 195 -100 796 282 514 4.213 .237 2.075
9 1658 804 83 171 1575 633 91 190 75 69 .408 112 1017 .296 .729 74 86 198 210 0 1410 300 1110 .705 1.419 -.505 -.505
10 291 383 86 170 205 213 93 190 68 62 .966 112 1017 .617 .559 74 86 213 225 0 671 298 373 1.82 .55 .864 .864
11 266 428 80 167 186 261 86 184 79 76 1.378 112 1017 .735 .527 74 86 228 240 0 750 292 458 2.462 .406 1.3 1.3
12 407 401 75 162 332 239 78 172 79 72 .705 112 1009 .516 .62 74 86 242 254 0 703 284 419 1.262 .792 .336 .336
13 282 382 75 163 207 219 79 173 70 63 .892 112 1013 .804 .649 74 86 257 269 0 670 285 385 1.86 .538 .895 .895
14 1886 766 80 169 1806 597 86 183 93 83 .308 112 1017 .27 .765 74 86 272 284 0 1343 296 1047 .58 1.725 -.787 -.787
15 244 406 84 183 160 223 89 196 79 69 1.354 112 1017 .811 .511 74 86 287 299 0 712 321 391 2.444 .409 1.289 1.289
16 269 389 88 196 181 193 97 210 75 60 1.179 112 1017 .744 .586 74 86 302 314 0 682 343 339 1.873 .534 .905 .905
17 1377 830 93 205 1284 625 101 222 91 86 .51 112 1017 .365 .722 74 86 317 329 0 1456 359 1097 .854 1.17 -.227 -.227
18 216 415 94 206 122 209 103 225 66 67 1.671 112 1017 1.11 .574 74 86 332 344 0 728 361 367 3.008 .332 1.589 1.589
19 511 619 87 198 424 421 93 216 83 79 .929 112 1017 .7 .657 74 86 347 359 0 1085 347 738 1.741 .575 .8 .8
20 291 374 83 183 208 191 85 199 78 66 .793 112 1017 .682 .62 74 86 362 374 0 656 321 335 1.611 .621 .688 .688

Total number of rows: 24192

Table truncated, full table size 2784 Kbytes.




Supplementary data files not provided

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