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Sample GSM71627 Query DataSets for GSM71627
Status Public on Aug 24, 2005
Title cell cycle-alpha factor, fkh1, fkh2 015min
Sample type RNA
 
Channel 1
Source name Reference Pool
Organism Saccharomyces cerevisiae
Characteristics Reference Pool
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 015 min
Organism Saccharomyces cerevisiae
Characteristics 015 min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/486.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 Aug 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)
GSE3182 Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth

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
1 109 170 57 47 52 123 66 49 50 58 1.829 225 1016 1.265 .691 116 133 102 119 0 189 52 137 2.635 .38 1.398
2 94 73 58 48 36 25 66 52 37 27 .733 225 741 .575 .761 116 133 119 136 0 81 53 28 .778 1.286 -.363
3 302 384 61 48 241 336 69 51 57 49 1.259 225 756 1.261 .896 116 133 136 153 0 427 53 374 1.552 .644 .634
4 131 126 63 49 68 77 70 53 42 32 .8 225 756 1.196 .908 116 133 154 171 0 140 54 86 1.265 .791 .339
5 149 164 63 48 86 116 71 50 43 42 1.071 225 756 1.249 .89 116 133 171 188 0 182 53 129 1.5 .667 .585
6 89 83 63 46 26 37 72 51 28 27 .778 225 756 .927 .76 116 133 189 206 0 92 51 41 1.577 .634 .657
7 60 40 61 44 null null 73 49 21 10 .417 225 756 .035 .073 116 133 206 223 0 44 49 null null null null
8 56 41 59 42 null null 73 47 21 15 .41 225 756 -.037 -.068 116 133 224 241 0 46 47 null null null null
9 60 44 54 43 6 1 65 45 28 11 .393 225 756 .036 .084 116 133 241 258 0 49 48 1 .167 6 -2.585
10 64 44 56 43 8 1 64 45 29 18 .5 225 746 .011 .024 116 133 259 276 0 49 48 1 .125 8 -3
11 56 45 59 43 null 2 67 46 14 18 .706 225 756 .023 .043 116 133 276 293 0 50 48 2 null null null
12 64 44 57 43 7 1 63 46 25 16 .326 225 756 -.011 -.025 116 133 294 311 0 49 48 1 .143 7 -2.807
13 62 47 56 43 6 4 63 45 24 19 .625 225 756 .229 .386 116 133 311 328 0 52 48 4 .667 1.5 -.585
14 63 45 56 43 7 2 63 44 23 16 .4 225 756 .008 .016 116 133 329 346 0 50 48 2 .286 3.5 -1.807
15 65 51 55 43 10 8 62 45 28 25 .66 225 756 .04 .047 116 133 346 363 0 57 48 9 .9 1.111 -.152
16 65 45 53 43 12 2 61 44 34 17 .444 225 756 .009 .021 116 133 364 381 0 50 48 2 .167 6 -2.585
17 92 52 53 43 39 9 62 44 32 20 .438 225 756 .14 .581 116 133 381 398 0 58 48 10 .256 3.9 -1.963
18 67 44 52 43 15 1 61 45 34 18 .379 225 756 .028 .069 116 133 399 416 0 49 48 1 .067 15 -3.907
19 60 46 48 44 12 2 58 46 31 17 .4 225 756 .025 .052 116 133 416 433 0 51 49 2 .167 6 -2.585
20 64 48 52 46 12 2 61 47 34 16 .5 225 756 .03 .062 116 133 434 451 0 53 51 2 .167 6 -2.585

Total number of rows: 9216

Table truncated, full table size 967 Kbytes.




Supplementary data files not provided
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