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Sample GSM75949 Query DataSets for GSM75949
Status Public on Sep 24, 2005
Title DES460 + 0.02% MMS - 90 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 = 90 min
Organism Saccharomyces cerevisiae
Characteristics time = 90 min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: DNA damage, MMS
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/6358.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 GPL2650
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 73 42 36 16 37 26 39 17 22 35 .8 193 1103 .581 .896 87 104 141 158 0 59 22 37 1 1 0
2 84 37 38 17 46 20 43 24 43 43 .444 193 841 .438 .793 87 104 159 176 0 52 23 29 .63 1.586 -.666
3 1652 1175 37 17 1615 1158 47 35 90 92 .715 193 841 .666 .943 87 104 176 193 0 1654 23 1631 1.01 .99 .014
4 82 44 37 18 45 26 64 63 30 34 .59 193 867 .53 .9 87 104 194 211 0 61 25 36 .8 1.25 -.322
5 1163 877 40 19 1123 858 72 57 84 88 .754 193 795 .688 .938 87 104 212 229 0 1235 26 1209 1.077 .929 .106
6 116 65 43 19 73 46 86 66 31 40 .675 193 795 .552 .93 87 104 227 244 0 91 26 65 .89 1.123 -.167
7 43 17 40 18 3 null 67 44 10 12 .402 193 841 .142 .319 87 104 245 262 0 23 25 null null null null
8 43 17 38 17 5 null 46 24 16 15 .364 193 851 .084 .192 87 104 262 279 0 23 23 null null null null
9 69 23 39 18 30 5 61 25 35 23 .258 193 892 .11 .431 87 104 280 297 0 32 25 7 .233 4.286 -2.1
10 50 20 40 17 10 3 60 22 24 27 .571 193 877 .096 .158 87 104 298 315 0 28 23 5 .5 2 -1
11 37 17 39 16 null 1 52 25 6 15 .5 193 877 .044 .066 87 104 315 332 0 23 22 1 null null null
12 39 16 38 16 1 null 53 25 7 14 1 193 877 .066 .088 87 104 333 350 0 22 22 null null null null
13 39 17 38 17 1 null 42 20 6 12 .778 193 877 .116 .233 87 104 350 367 0 23 23 null null null null
14 36 16 38 16 null null 40 19 6 14 1.077 193 877 .022 .036 87 104 368 385 0 22 22 null null null null
15 34 16 40 18 null null 57 23 1 8 .923 193 877 .017 .026 87 104 385 402 0 22 25 null null null null
16 37 16 42 18 null null 61 24 2 10 .778 193 902 .066 .096 87 104 403 420 0 22 25 null null null null
17 37 18 38 16 null 2 44 18 4 23 1 193 877 .012 .014 87 104 421 438 0 25 22 3 null null null
18 37 18 35 16 2 2 36 16 10 23 .667 193 877 .094 .142 87 104 438 455 0 25 22 3 1.5 .667 .585
19 40 18 36 16 4 2 38 17 18 23 .684 193 877 .045 .071 87 104 456 473 0 25 22 3 .75 1.333 -.415
20 68 21 38 17 30 4 51 29 31 26 .282 193 841 .109 .69 88 105 473 490 0 29 23 6 .2 5 -2.322

Total number of rows: 9216

Table truncated, full table size 976 Kbytes.




Supplementary data files not provided
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