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Sample GSM96015 Query DataSets for GSM96015
Status Public on Feb 25, 2006
Title Ovarian Cell Line HEY
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 HEY
Organism Homo sapiens
Characteristics Ovarian Cell Line HEY
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-line, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2000-04/5102.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
1 691 895 86 52 605 843 91 57 82 85 1.302 112 1225 1.295 .932 81 93 48 60 0 839 49 790 1.306 .766 .385
2 634 592 86 52 548 540 91 60 81 81 .976 112 1005 .875 .9 81 93 63 75 0 555 49 506 .923 1.083 -.115
3 491 916 85 52 406 864 90 58 76 87 1.891 112 1005 1.862 .868 81 93 78 90 0 858 49 810 1.994 .501 .996
4 312 123 87 52 225 71 94 59 77 71 .309 112 1005 .307 .724 81 93 93 105 0 115 49 67 .296 3.382 -1.758
5 958 671 89 52 869 619 105 65 80 84 .707 112 1005 .64 .909 81 93 108 120 0 629 49 580 .667 1.498 -.583
6 685 802 92 54 593 748 107 67 91 92 1.228 112 1005 1.152 .926 81 93 123 135 0 752 51 701 1.182 .846 .241
7 350 388 89 53 261 335 97 60 66 67 1.191 112 1005 1.154 .907 81 93 138 150 0 364 50 314 1.203 .831 .266
8 312 195 88 54 224 141 91 57 58 56 .679 112 1005 .653 .896 81 93 153 165 0 183 51 132 .59 1.695 -.762
9 2420 3465 87 53 2333 3412 91 58 82 91 1.387 112 1005 1.37 .922 81 93 168 180 0 3247 50 3197 1.37 .73 .455
10 537 154 87 53 450 101 90 60 77 71 .225 112 1005 .214 .817 81 93 183 195 0 144 50 95 .21 4.755 -2.249
11 283 463 88 53 195 410 90 62 69 81 2.02 112 1005 1.84 .904 81 93 198 210 0 434 50 384 1.97 .508 .978
12 918 5437 88 54 830 5383 91 63 80 96 5.717 112 1005 5.764 .884 81 93 213 225 0 5095 51 5044 6.077 .165 2.603
13 463 612 88 54 375 558 94 67 61 78 1.336 112 1005 1.293 .864 81 93 228 240 0 573 51 523 1.394 .717 .48
14 3669 9551 89 54 3580 9497 95 64 85 97 2.46 112 1005 2.438 .905 81 93 243 255 0 8950 51 8899 2.486 .402 1.314
15 351 315 91 52 260 263 97 63 77 76 .794 112 1005 .96 .727 81 93 258 270 0 295 49 246 .948 1.055 -.077
16 595 319 96 53 499 266 107 67 70 74 .485 112 1005 .525 .786 81 93 273 285 0 299 50 249 .5 2.002 -1.001
17 3153 8660 99 54 3054 8606 110 71 85 97 2.742 112 1005 2.607 .917 81 93 288 300 0 8115 51 8064 2.641 .379 1.401
18 317 299 96 54 221 245 108 73 71 79 1.013 112 1005 1.201 .861 81 93 303 315 0 280 51 230 1.039 .963 .055
19 1337 1943 95 53 1242 1890 105 65 78 83 1.295 112 1005 1.34 .898 81 93 318 330 0 1821 50 1771 1.426 .701 .512
20 802 1112 95 52 707 1060 105 64 75 83 1.452 112 1009 1.405 .955 81 93 333 345 0 1042 49 993 1.405 .712 .49

Total number of rows: 24192

Table truncated, full table size 2600 Kbytes.




Supplementary data files not provided
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