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Sample GSM75984 Query DataSets for GSM75984
Status Public on Sep 24, 2005
Title dun1- + 0.02% MMs - 30 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 = 30 min
Organism Saccharomyces cerevisiae
Characteristics time = 30 min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: DNA damage, MMS
Image: http://smd.stanford.edu/MicroArray/gifs/1999-10/8526.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
1 196 185 12 15 184 170 14 16 92 83 .37 145 1206 1.98 .8 100 115 134 149 0 73 5 68 .37 2.706 -1.436
2 85 223 12 15 73 208 13 16 52 64 1.17 145 1049 5.87 .91 99 114 151 166 0 88 5 83 1.137 .88 .185
3 810 2136 10 14 800 2122 12 15 94 96 1.06 145 1071 6.03 .93 99 114 169 184 0 847 5 842 1.053 .95 .074
4 39 92 10 14 29 78 12 15 41 30 .62 145 1071 5.36 .81 99 114 187 202 0 36 5 31 1.069 .935 .096
5 532 1674 9 13 523 1661 11 15 86 94 1.26 145 1071 7.13 .94 99 114 205 220 0 664 5 659 1.26 .794 .333
6 32 75 9 13 23 62 11 14 48 39 .54 145 1049 6.57 .91 99 114 223 238 0 29 5 24 1.043 .958 .061
7 11 14 9 13 2 1 11 14 37 26 .34 145 993 .18 .07 99 114 240 255 0 5 5 null null null null
8 10 13 10 12 null 1 11 14 31 28 .37 145 989 .19 .09 99 114 256 271 0 5 4 1 null null null
9 11 13 10 13 1 null 11 14 34 21 .27 145 1012 .11 .06 99 114 274 289 0 5 5 null null null null
10 12 14 10 13 2 1 12 15 30 23 .44 145 991 .3 .12 99 114 292 307 0 5 5 null null null null
11 11 14 10 12 1 2 12 14 35 24 .25 145 1025 .31 .13 98 113 310 325 0 5 4 1 1 1 0
12 11 12 10 12 1 null 12 14 32 21 .34 145 1054 .18 .08 98 113 328 343 0 4 4 null null null null
13 11 14 10 13 1 1 13 15 28 27 .32 145 1058 .02 .01 98 113 346 361 0 5 5 null null null null
14 11 13 10 14 1 -1 13 17 30 14 .35 145 1049 .84 .35 98 113 363 378 0 5 5 null null null null
15 10 14 10 14 null null 13 17 24 21 .4 145 993 .03 .01 98 113 381 396 0 5 5 null null null null
16 11 14 10 13 1 1 12 15 31 22 .4 145 969 -.09 -.04 98 113 396 411 0 5 5 null null null null
17 11 12 10 12 1 null 12 14 31 21 .22 145 1043 .12 .06 98 113 413 428 0 4 4 null null null null
18 10 13 10 12 null 1 11 14 24 30 .4 145 1067 1.08 .35 98 113 433 448 0 5 4 1 null null null
19 12 13 10 12 2 1 11 13 35 21 .29 145 986 .3 .13 98 113 451 466 0 5 4 1 .5 2 -1
20 10 12 9 12 1 null 11 13 31 19 .4 145 1014 0 0 97 112 465 480 0 4 4 null null null null

Total number of rows: 9216

Table truncated, full table size 923 Kbytes.




Supplementary data files not provided
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