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Sample GSM96008 Query DataSets for GSM96008
Status Public on Feb 25, 2006
Title Ovarian Cell Line MES-OV
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 Cell Line MES-OV
Organism Homo sapiens
Characteristics Ovarian Cell Line MES-OV
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-line, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2000-04/4330.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 (1)
GSE4197 Ovarian 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 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 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 2406 2317 246 121 2160 2196 257 128 82 88 .989 112 1233 .936 .94 78 90 104 116 0 2234 117 2117 .98 1.02 -.029
2 2484 2340 247 122 2237 2218 258 128 87 87 .927 112 1017 .866 .906 78 90 119 131 0 2256 118 2138 .956 1.046 -.065
3 1597 2233 245 121 1352 2112 252 126 76 85 1.516 112 1017 1.373 .906 78 90 134 146 0 2153 117 2036 1.506 .664 .591
4 884 303 247 120 637 183 253 126 74 75 .286 112 1017 .231 .808 78 90 149 161 0 292 116 176 .277 3.61 -1.852
5 4241 4003 252 123 3989 3880 270 141 90 98 .983 112 1017 .89 .922 78 90 164 176 0 3859 119 3741 .938 1.066 -.093
6 2236 2310 251 124 1985 2186 269 140 98 100 1.087 112 1017 1.014 .927 78 90 179 191 0 2227 120 2108 1.062 .942 .086
7 862 648 246 123 616 525 258 133 65 74 .803 112 1017 .716 .873 78 90 194 206 0 625 119 506 .822 1.217 -.283
8 949 1241 250 123 699 1118 260 135 73 83 1.372 112 1017 1.331 .869 78 90 209 221 0 1197 119 1078 1.542 .648 .625
9 7595 7144 249 122 7346 7022 258 133 82 88 .926 112 1017 .862 .916 78 90 224 236 0 6888 118 6770 .922 1.085 -.118
10 1616 360 246 123 1370 237 255 129 75 65 .158 112 1017 .145 .835 78 90 239 251 0 347 119 229 .167 5.996 -2.584
11 1044 430 248 122 796 308 252 126 75 74 .37 112 1017 .329 .893 78 90 254 266 0 415 118 297 .373 2.681 -1.423
12 4369 6306 249 121 4120 6185 256 127 86 95 1.419 112 1017 1.289 .903 78 90 269 281 0 6080 117 5963 1.447 .691 .533
13 1879 1939 250 122 1629 1817 263 132 68 77 1.008 112 1017 .965 .912 78 90 284 296 0 1869 118 1752 1.075 .93 .105
14 13290 11616 251 127 13039 11489 266 135 85 91 .819 112 1021 .777 .925 79 91 299 311 0 11200 122 11077 .85 1.177 -.235
15 1322 1150 256 131 1066 1019 269 137 78 81 .968 112 1025 .845 .923 79 91 314 326 0 1109 126 982 .922 1.085 -.118
16 2227 4191 256 132 1971 4059 270 148 75 83 1.951 112 1025 1.847 .923 79 91 330 342 0 4041 127 3913 1.986 .504 .99
17 8322 14510 257 133 8065 14377 269 150 88 92 1.658 112 1017 1.598 .928 79 91 345 357 0 13990 128 13862 1.719 .582 .781
18 826 553 260 134 566 419 272 142 69 77 .748 112 1017 .613 .865 79 91 360 372 0 533 129 404 .714 1.401 -.487
19 4736 5379 260 132 4476 5247 365 318 85 91 1.087 112 1017 1.056 .917 79 91 375 387 0 5186 127 5059 1.13 .885 .177
20 1858 1662 260 133 1598 1529 411 362 82 85 .863 112 1017 .993 .868 79 91 390 402 0 1602 128 1474 .923 1.084 -.116

Total number of rows: 24192

Table truncated, full table size 2769 Kbytes.




Supplementary data files not provided
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