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Sample GSM79618 Query DataSets for GSM79618
Status Public on Oct 22, 2005
Title wt vs aft1up: met
Sample type RNA
 
Channel 1
Source name wt
Organism Saccharomyces cerevisiae
Characteristics wt
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name aft1up
Organism Saccharomyces cerevisiae
Characteristics aft1up
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Martel, Martel
Image: http://smd.stanford.edu/MicroArray/gifs/1999-10/8662.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 Oct 21, 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 GPL59
Series (2)
GSE3496 Iron uptake in yeast
GSE4196 Iron uptake experiments in yeast

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 4487 5941 2345 1940 2142 4001 null null 0 0 null null null 1.04 .98 61 70 74 83 0 3454 1127 2327 1.086 .92 .12
2 5325 7088 2279 1778 3046 5310 null null 0 0 null null null 1.08 .97 61 70 84 93 0 4120 1033 3087 1.013 .987 .019
3 6656 9937 2338 1750 4318 8187 null null 0 0 null null null .97 .97 61 70 94 103 0 5777 1017 4760 1.102 .907 .141
4 5118 5497 2126 1649 2992 3848 null null 0 0 null null null 1.09 .59 61 70 104 113 0 3195 958 2237 .748 1.338 -.42
5 4749 6266 2040 1455 2709 4811 null null 0 0 null null null 1.03 .96 61 70 114 123 0 3643 845 2798 1.033 .968 .047
6 4616 6140 2143 1642 2473 4498 null null 0 0 null null null .95 .95 61 70 124 133 0 3569 954 2615 1.057 .946 .081
7 4193 5063 2058 1473 2135 3590 null null 0 0 null null null 1.06 .97 61 70 134 143 0 2943 856 2087 .978 1.023 -.033
8 4548 3669 2098 1457 2450 2212 null null 0 0 null null null 2.19 .94 61 70 144 153 0 2133 847 1286 .525 1.905 -.93
9 4133 6004 2110 1476 2023 4528 null null 0 0 null null null .85 .97 61 70 154 163 0 3490 858 2632 1.301 .769 .38
10 4118 5147 2006 1534 2112 3613 null null 0 0 null null null 1.1 .98 61 70 164 173 0 2992 891 2101 .995 1.005 -.008
11 4421 5815 2056 1620 2365 4195 null null 0 0 null null null 1.01 .96 61 70 174 183 0 3380 941 2439 1.031 .97 .044
12 5036 6701 2119 1683 2917 5018 null null 0 0 null null null 1.03 .96 61 70 184 193 0 3895 978 2917 1 1 0
13 2866 2662 2148 1524 718 1138 null null 0 0 null null null .93 .95 61 70 194 203 0 1547 886 661 .921 1.086 -.119
14 3260 3296 2110 1330 1150 1966 null null 0 0 null null null .98 .93 61 70 204 213 0 1916 773 1143 .994 1.006 -.009
15 4072 4667 2124 1476 1948 3191 null null 0 0 null null null 1.08 .97 61 70 214 223 0 2713 858 1855 .952 1.05 -.071
16 5400 7521 2112 1408 3288 6113 null null 0 0 null null null .99 .97 61 70 224 233 0 4372 818 3554 1.081 .925 .112
17 4318 5275 2136 1372 2182 3903 null null 0 0 null null null .99 .97 61 70 234 243 0 3066 797 2269 1.04 .962 .056
18 4691 4502 2200 1404 2491 3098 null null 0 0 null null null 1.51 .97 61 70 244 253 0 2617 816 1801 .723 1.383 -.468
19 28432 5390 2298 1472 26134 3918 null null 0 0 null null null 8.63 .8 61 70 254 263 0 3133 855 2278 .087 11.472 -3.52
20 8414 12946 2253 1570 6161 11376 null null 0 0 null null null .93 .91 61 70 264 273 0 7526 912 6614 1.074 .932 .102

Total number of rows: 7680

Table truncated, full table size 897 Kbytes.




Supplementary data files not provided

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