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Sample GSM96036 Query DataSets for GSM96036
Status Public on Feb 25, 2006
Title Ovarian Ca OV312
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 OV312
Organism Homo sapiens
Characteristics Ovarian Ca OV312
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Solid tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2000-04/5103.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
1 498 613 64 61 434 552 66 68 75 75 1.172 112 1233 1.282 .916 113 125 51 63 0 887 88 798 1.839 .544 .879 .879
2 414 421 65 61 349 360 66 65 72 72 .984 112 1017 .964 .925 113 125 66 78 0 609 88 521 1.492 .67 .577 .577
3 300 148 65 59 235 89 66 61 75 69 .343 112 1017 .365 .85 113 125 81 93 0 214 85 129 .548 1.826 -.868 -.868
4 273 254 66 57 207 197 68 60 88 86 .934 112 1017 .862 .847 113 125 96 108 0 367 82 285 1.376 .727 .461 .461
5 610 173 68 61 542 112 78 67 83 74 .197 112 1017 .174 .797 114 126 111 123 0 250 88 162 .299 3.346 -1.742 -1.742
6 387 336 69 64 318 272 82 69 77 82 .815 112 1017 .779 .92 114 126 126 138 0 486 93 393 1.237 .808 .307 .307
7 238 163 70 65 168 98 82 70 56 57 .548 112 1013 .517 .89 114 126 140 152 0 236 94 142 .844 1.185 -.245 -.245
8 250 165 71 65 179 100 77 67 64 61 .577 112 1017 .503 .899 114 126 155 167 0 239 94 145 .808 1.238 -.308 -.308
9 2928 693 72 64 2856 629 79 68 82 80 .217 112 1017 .21 .929 114 126 170 182 0 1002 93 910 .319 3.14 -1.651 -1.651
10 417 133 72 64 345 69 78 67 69 58 .22 112 1017 .208 .875 114 126 185 197 0 192 93 100 .289 3.457 -1.79 -1.79
11 253 310 70 63 183 247 74 65 69 74 1.234 112 1017 1.199 .887 114 126 200 212 0 448 91 357 1.952 .512 .965 .965
12 642 514 70 64 572 450 75 68 75 79 .788 112 1017 .73 .961 114 126 215 227 0 743 93 651 1.138 .879 .186 .186
13 350 336 69 63 281 273 76 67 69 67 .962 112 1017 .918 .917 114 126 230 242 0 486 91 395 1.405 .712 .491 .491
14 2618 1058 68 63 2550 995 75 66 83 83 .38 112 1017 .377 .928 114 126 245 257 0 1530 91 1439 .564 1.772 -.825 -.825
15 255 227 69 63 186 164 75 65 73 76 .84 112 1017 .754 .875 114 126 260 272 0 328 91 237 1.275 .784 .351 .351
16 355 255 71 65 284 190 82 69 66 64 .601 112 1017 .619 .923 114 126 275 287 0 369 94 275 .968 1.034 -.048 -.048
17 1836 1356 71 67 1765 1289 82 71 80 83 .73 112 1017 .713 .939 114 126 290 302 0 1961 97 1864 1.056 .947 .079 .079
18 177 183 71 67 106 116 79 70 70 64 .979 112 1017 .736 .764 114 126 305 317 0 265 97 168 1.583 .632 .662 .662
19 834 612 69 66 765 546 72 67 78 81 .683 112 1017 .668 .91 114 126 320 332 0 885 95 790 1.032 .969 .046 .046
20 309 338 68 66 241 272 71 67 69 75 1.157 112 1009 1.052 .925 114 126 334 346 0 489 95 393 1.632 .613 .707 .707

Total number of rows: 24192

Table truncated, full table size 2678 Kbytes.




Supplementary data files not provided

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