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Sample GSM75967 Query DataSets for GSM75967
Status Public on Sep 24, 2005
Title DES460 + 0.02% MMS - 5 min
Sample type RNA
 
Channel 1
Source name time = 0 min
Organism Saccharomyces cerevisiae
Characteristics time = 0 min
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name time = 5 min
Organism Saccharomyces cerevisiae
Characteristics time = 5 min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: DNA damage, MMS
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/6344.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 Sep 23, 2005
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 GPL51
Series (1)
GSE3358 DNA damage responses and Mec1p

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
1 405 153 75 45 330 108 85 48 80 77 .355 145 1197 .268 .781 126 141 107 122 0 143 42 101 .305 3.274 -1.711
2 156 149 75 48 81 101 86 50 23 31 1.1 145 1036 1.138 .963 125 140 124 139 0 139 45 94 1.164 .859 .219
3 999 1179 68 44 931 1135 69 45 72 73 1.19 145 1017 1.205 .971 125 140 142 157 0 1100 41 1059 1.138 .879 .186
4 160 166 60 38 100 128 62 40 27 37 1.238 145 1009 1.292 .976 125 140 159 174 0 155 35 119 1.195 .837 .256
5 622 731 54 35 568 696 57 38 57 67 1.223 145 1039 1.196 .976 124 139 177 192 0 682 33 650 1.144 .874 .193
6 100 96 53 34 47 62 54 36 17 27 1.273 145 1017 1.166 .969 124 139 195 210 0 90 32 58 1.231 .812 .3
7 46 16 52 30 null null 53 30 2 6 .539 145 1027 null null 124 139 212 227 0 15 28 -13 null null null
8 64 33 52 28 12 5 53 29 24 28 .661 145 1039 .3 .361 123 138 230 245 0 31 26 5 .389 2.572 -1.363
9 50 32 52 30 null 2 53 30 5 18 1 145 1027 .126 .138 123 138 247 262 0 30 28 2 null null null
10 50 30 50 31 null null 51 31 7 20 1.462 145 1030 .328 .299 123 138 265 280 0 28 29 -1 null null null
11 48 33 47 31 1 2 48 31 8 15 .8 145 1039 .072 .099 122 137 283 298 0 31 29 2 1.866 .536 .9
12 47 32 46 34 1 null 47 34 6 6 1.333 145 1036 .174 .176 122 137 300 315 0 30 32 -2 null null null
13 49 35 45 31 4 4 46 32 10 22 1 145 1017 null null 122 137 318 333 0 33 29 4 .933 1.072 -.1
14 38 25 39 25 null null 41 27 8 13 1.4 145 1009 .042 .049 122 137 335 350 0 23 23 0 null null null
15 33 20 33 21 null null 35 23 6 22 1.357 145 1039 .033 .03 121 136 353 368 0 19 20 -1 null null null
16 32 19 33 21 null null 35 24 9 14 1.2 145 1017 null null 121 136 371 386 0 18 20 -2 null null null
17 36 22 34 21 2 1 35 23 12 19 .818 145 1019 .091 .109 121 136 388 403 0 21 20 1 .467 2.143 -1.1
18 35 21 33 22 2 null 34 22 8 15 .833 145 1026 .054 .061 120 135 406 421 0 20 21 -1 null null null
19 37 24 35 22 2 2 38 24 12 19 1.143 145 1017 .269 .216 120 135 423 438 0 22 21 2 .933 1.072 -.1
20 40 26 38 24 2 2 41 25 11 22 1.273 145 1040 .096 .111 120 135 441 456 0 24 22 2 .933 1.072 -.1

Total number of rows: 9216

Table truncated, full table size 981 Kbytes.




Supplementary data files not provided
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