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Sample GSM75978 Query DataSets for GSM75978
Status Public on Sep 24, 2005
Title dun1- + 0.02% MMS - 120 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 = 120 min
Organism Saccharomyces cerevisiae
Characteristics time = 120 min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: DNA damage, MMS
Image: http://smd.stanford.edu/MicroArray/gifs/1999-10/8521.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
1 193 168 11 5 182 163 14 7 89 88 .53 145 1206 1.37 .87 88 103 139 154 0 103 3 100 .549 1.82 -.864
2 68 98 10 5 58 93 12 6 59 68 .89 145 1027 2.11 .91 87 102 156 171 0 60 3 57 .983 1.018 -.025
3 777 1457 10 5 767 1452 12 7 89 96 1.17 145 1027 2.8 .94 87 102 173 188 0 893 3 890 1.16 .862 .215
4 31 40 10 5 21 35 12 8 48 44 .72 145 1027 2.42 .83 87 102 190 205 0 24 3 21 1 1 0
5 427 763 9 5 418 758 11 7 88 87 1.2 145 1040 2.65 .94 86 101 208 223 0 468 3 465 1.112 .899 .154
6 27 63 9 4 18 59 10 6 49 53 .93 145 1017 3.65 .47 86 101 225 240 0 38 2 36 2 .5 1
7 10 5 8 4 2 1 10 5 32 31 .29 145 1027 .13 .11 86 101 242 257 0 3 2 1 .5 2 -1
8 10 7 9 4 1 3 10 6 32 46 .42 145 1049 -.02 -.02 85 100 260 275 0 4 2 2 2 .5 1
9 11 4 8 4 3 null 10 6 40 30 .35 145 1017 -.03 -.04 85 100 277 292 0 2 2 null null null null
10 9 4 8 4 1 null 10 6 30 30 .45 145 1027 .17 .17 85 100 294 309 0 2 2 null null null null
11 8 5 8 4 null 1 10 6 26 34 .36 145 1017 .18 .16 85 100 312 327 0 3 2 1 null null null
12 11 7 8 4 3 3 10 5 42 39 .37 145 1027 .18 .14 84 99 329 344 0 4 2 2 .667 1.5 -.585
13 10 5 8 4 2 1 9 5 32 34 .56 145 1027 -.15 -.1 84 99 346 361 0 3 2 1 .5 2 -1
14 10 5 8 4 2 1 9 5 35 32 .38 145 1027 -.04 -.04 84 99 363 378 0 3 2 1 .5 2 -1
15 9 7 8 4 1 3 9 5 31 32 1.1 145 1040 .64 .29 83 98 381 396 0 4 2 2 2 .5 1
16 8 5 8 4 null 1 9 5 25 28 .63 145 1017 .21 .16 83 98 398 413 0 3 2 1 null null null
17 8 5 8 4 null 1 9 5 25 32 .94 145 1027 .14 .13 83 98 415 430 0 3 2 1 null null null
18 9 4 7 4 2 null 9 5 38 32 .25 145 1049 .09 .11 82 97 433 448 0 2 2 null null null null
19 9 4 7 4 2 null 9 5 41 23 .39 145 1017 -.07 -.07 82 97 450 465 0 2 2 null null null null
20 7 4 7 3 null 1 8 5 32 43 .42 145 1027 -.01 -.01 82 97 467 482 0 2 1 1 null null null

Total number of rows: 9216

Table truncated, full table size 893 Kbytes.




Supplementary data files not provided
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