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Sample GSM97265 Query DataSets for GSM97265
Status Public on Feb 25, 2006
Title Ovarian Ca OV151
Sample type RNA
 
Channel 1
Source name CRB1
Organism Homo sapiens
Characteristics CRB1
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Ovarian Ca OV151
Organism Homo sapiens
Characteristics Ovarian Ca OV151
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Solid tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5348.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 (1)
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
1 376 469 59 211 317 258 65 248 60 51 .928 156 1152 .598 .88 56 70 56 70 0 768 345 423 1.334 .749 .416 .416
2 437 480 65 216 372 264 74 235 66 56 .739 156 985 .521 .849 55 69 73 87 0 786 354 432 1.161 .861 .216 .216
3 274 354 69 234 205 120 77 252 51 35 .727 156 997 .597 .82 55 69 91 105 0 580 383 197 .961 1.041 -.057 -.057
4 305 419 70 247 235 172 77 268 57 38 .9 156 985 .709 .841 55 69 108 122 0 686 404 282 1.2 .833 .263 .263
5 450 555 66 245 384 310 75 269 62 48 .911 156 987 .761 .909 55 69 126 140 0 909 401 508 1.323 .756 .404 .404
6 434 545 57 217 377 328 69 260 66 63 .955 156 985 .78 .903 55 69 143 157 0 893 355 538 1.427 .701 .513 .513
7 175 371 54 202 121 169 63 238 48 37 1.45 156 968 1.164 .833 55 69 161 175 0 608 331 277 2.289 .437 1.195 1.195
8 1318 589 50 195 1268 394 54 201 71 51 .351 156 968 .31 .934 55 69 177 191 0 965 319 646 .509 1.963 -.973 -.973
9 387 737 48 205 339 532 52 212 71 61 1.765 156 935 1.325 .893 57 71 196 210 0 1208 336 872 2.572 .389 1.363 1.363
10 1538 1148 47 207 1491 941 51 235 78 58 .683 156 912 .575 .935 57 71 214 228 0 1881 339 1542 1.034 .967 .049 .049
11 515 469 44 200 471 269 48 230 68 50 .641 156 932 .525 .895 55 69 230 244 0 768 327 441 .936 1.068 -.095 -.095
12 452 454 41 195 411 259 45 221 67 48 .639 156 958 .576 .881 55 69 247 261 0 744 319 425 1.034 .967 .048 .048
13 258 489 40 196 218 293 42 204 66 51 1.496 156 958 1.254 .913 55 69 265 279 0 801 321 480 2.202 .454 1.139 1.139
14 213 418 37 203 176 215 39 209 58 48 1.376 156 958 1.072 .802 55 69 282 296 0 685 332 353 2.006 .499 1.004 1.004
15 1396 935 37 201 1359 734 39 213 71 58 .61 156 1024 .525 .949 54 68 300 314 0 1532 329 1203 .885 1.13 -.176 -.176
16 221 490 38 209 183 281 40 221 69 48 1.465 156 1013 1.521 .818 54 68 319 333 0 803 342 461 2.519 .397 1.333 1.333
17 237 588 38 211 199 377 43 220 63 50 1.388 156 999 1.116 .317 54 68 337 351 0 963 345 618 3.106 .322 1.635 1.635
18 1160 524 39 222 1121 302 44 230 80 46 .297 156 988 .258 .804 54 68 355 369 0 859 363 496 .442 2.26 -1.176 -1.176
19 587 1104 40 233 547 871 43 240 73 65 1.425 156 985 1.647 .857 54 68 372 386 -100 1809 381 1428 2.611 .383 1.384
20 412 632 38 240 374 392 42 269 64 46 1.197 156 997 .899 .788 54 68 390 404 -100 1036 393 643 1.719 .582 .782

Total number of rows: 9216

Table truncated, full table size 1053 Kbytes.




Supplementary data files not provided
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