|
Status |
Public on Oct 25, 2005 |
Title |
WT vs lpz8 null cells in low Cu |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
WT
|
Organism |
Saccharomyces cerevisiae |
Characteristics |
WT
|
Extracted molecule |
total RNA |
Label |
Cy3
|
|
|
Channel 2 |
Source name |
lpz8 null cells in low Cu
|
Organism |
Saccharomyces cerevisiae |
Characteristics |
lpz8 null cells in low Cu
|
Extracted molecule |
total RNA |
Label |
Cy5
|
|
|
|
Description |
Simple annotation: Metals, Copper Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/3022.gif
|
Data processing |
LOG_RAT2N_MEDIAN is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
|
|
|
Submission date |
Oct 24, 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 |
GPL65 |
Series (1) |
GSE3502 |
Haa1 regulated transcription |
|
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 |