|
| Status |
Public on Jul 25, 2001 |
| Title |
Sydney strian genomic DNA vs astra/tigr ref |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
1ug TIGR genomic DNA, 1ug Astra genomic DNA
|
| Organism |
Helicobacter pylori |
| Extracted molecule |
genomic DNA |
| |
|
| Channel 2 |
| Source name |
2 ug Sydney Genomic DNA (wizard prep)
|
| Organism |
Helicobacter pylori |
| Extracted molecule |
genomic DNA |
| |
|
| |
| Description |
Category: Genomic DNA
Subcategory: Strain Comparison
Scanning Software: ScanAlyze
Software version: 2.33
Scanning parameters:
Lot batch = hp2034
|
| |
|
| Submission date |
Jul 25, 2001 |
| Last update date |
Nov 21, 2005 |
| 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 |
GPL15 |
| Series (2) |
| GSE6 |
Genetic diversity among Helicobacter pylori strains |
| GSE3479 |
Helicobacter pylori bacterial populations |
|
| Data table header descriptions |
| ID_REF |
|
| CH1B_MEAN |
mean channel 1 background |
| CH1B_MEDIAN |
median channel 1 background |
| CH1D_MEAN |
difference between CH1I_MEAN and CH1B_MEAN |
| CH2I_MEAN |
mean channel 2 signal |
| CH2D_MEAN |
difference of CH2I_MEAN and CH2B_MEAN |
| CH2B_MEAN |
mean of channel 2 background |
| CH2B_MEDIAN |
median of channel 2 background |
| CH2BN_MEDIAN |
normalized CH2B_MEDIAN |
| CH2DN_MEAN |
normalized CH2D_MEAN |
| CH2IN_MEAN |
normalized CH2I_MEAN |
| CORR |
simple correlation coefficient of channel 1 and channel 2 pixels |
| FLAG |
user defined flag (default=0) |
| VALUE |
same as UNF_VALUE but with flagged values removed |
| PIX_RAT2_MEDIAN |
|
| PERGTBCH1I_1SD |
standard deviation of fraction of pixels greater than CH1B_MEAN |
| PERGTBCH2I_1SD |
standard deviation of fraction of pixels greater than CH2B_MEAN |
| RAT1_MEAN |
ratio of CH1D_MEAN to CH2D_MEAN |
| RAT1N_MEAN |
ratio of CH1DN_MEAN to CH2DN_MEAN |
| RAT2_MEAN |
ratio of CH2D_MEAN to CH1D_MEAN |
| RAT2N_MEAN |
ratio of CH2DN_MEAN and CH1DN_MEAN |
| REGR |
slope of the simple regression line of channel 2 to channel 1 pixels |
| TOT_BPIX |
total number of background pixels |
| TOT_SPIX |
total number of signal (spot) pixels |
| TOP |
vertical, short-axis spot ellipse minimum pixel coordinate |
| BOT |
vertical, short-axis spot ellipse maximum pixel coordinate |
| LEFT |
horizontal, long-axis spot ellipse minimum pixel coordinate |
| RIGHT |
horizontal, long-axis spot ellipse maximum pixel coordinate |
| UNF_VALUE |
aka LOG_RAT2N_MEAN, or log2 of ratio of CH2DN_MEAN and CH1DN_MEAN |
