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Sample GSM75958 Query DataSets for GSM75958
Status Public on Sep 24, 2005
Title MHY1 (dun1) + heat 20 min
Sample type RNA
 
Channel 1
Source name time = 0 min (at 30 degrees)
Organism Saccharomyces cerevisiae
Characteristics time = 0 min (at 30 degrees)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name time = 20 min (at 37 degrees)
Organism Saccharomyces cerevisiae
Characteristics time = 20 min (at 37 degrees)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Stress, Heat-shock
Image: http://smd.stanford.edu/MicroArray/gifs/1999-10/813.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 67 46 33 39 34 7 48 42 51 31 .333 225 1016 -.03 -.079 107 124 74 91 0 57 48 9 .265 3.778 -1.918
2 67 62 40 43 27 19 58 48 49 38 .494 225 735 .021 .04 107 124 92 109 0 77 53 24 .889 1.125 -.17
3 363 149 42 44 321 105 57 48 77 77 .333 225 745 .236 .757 106 123 110 127 0 184 54 130 .405 2.469 -1.304
4 76 58 36 42 40 16 50 47 50 31 .487 225 731 .241 .494 106 123 127 144 0 72 52 20 .5 2 -1
5 358 325 33 41 325 284 48 45 83 78 .832 225 746 .7 .792 106 123 145 162 0 401 51 350 1.077 .929 .107
6 108 120 33 44 75 76 83 109 49 36 .5 225 756 .918 .826 105 122 163 180 -100 148 54 94 1.253 .798 .326
7 48 48 39 45 9 3 84 110 33 19 .466 225 746 .003 .006 105 122 180 197 -100 59 56 3 .333 3 -1.585
8 48 45 37 45 11 null 82 110 36 19 .46 225 756 .033 .066 105 122 198 215 -100 56 56 null null null null
9 48 48 35 44 13 4 48 46 36 21 .421 225 720 .005 .011 105 122 216 233 -100 59 54 5 .385 2.6 -1.379
10 44 49 33 47 11 2 48 48 34 19 .528 225 746 .077 .17 104 121 233 250 -100 60 58 2 .182 5.5 -2.459
11 52 49 37 48 15 1 51 50 37 16 .405 225 756 .021 .047 104 121 251 268 -100 60 59 1 .067 15 -3.907
12 55 48 38 47 17 1 50 50 37 17 .395 225 720 .012 .029 104 121 269 286 -100 59 58 1 .059 17 -4.087
13 53 46 35 44 18 2 49 47 38 15 .377 225 756 -.028 -.07 103 120 286 303 -100 57 54 3 .167 6 -2.585
14 53 49 37 44 16 5 52 47 37 24 .409 225 756 -.005 -.011 103 120 304 321 -100 60 54 6 .375 2.667 -1.415
15 48 49 38 47 10 2 51 49 37 18 .388 225 731 -.027 -.053 103 120 321 338 -100 60 58 2 .2 5 -2.322
16 52 44 37 46 15 null 50 49 39 13 .375 225 735 -.024 -.059 103 120 339 356 -100 54 57 null null null null
17 44 46 35 44 9 2 49 48 38 19 .539 225 745 .037 .072 102 119 357 374 -100 57 54 3 .333 3 -1.585
18 54 47 38 46 16 1 51 49 37 20 .387 225 731 .07 .167 102 119 374 391 -100 58 57 1 .063 16 -4
19 50 46 36 46 14 null 50 50 38 14 .446 225 746 .089 .166 102 119 392 409 -100 57 57 null null null null
20 53 46 39 45 14 1 53 48 38 15 .484 225 756 -.006 -.016 101 118 410 427 -100 57 56 1 .071 14 -3.807

Total number of rows: 9216

Table truncated, full table size 963 Kbytes.




Supplementary data files not provided
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