Files included in export:
The job information submitted to tranSMART. The job information gives an overview of the input data for the analysis. At parameters it shows the jobType to indicate the type of analysis and which image will be produced. The selected variables are displayed using the full concept path names for each of them.
Variables selected: groupVariable and regionVariable show the concept paths of the variables used for grouping and the aCGH region, respectively. variablesConceptPaths gives a summary of all used concept paths.
This file contains the data that was used to do the analysis. Depending on what was uploaded to tranSMART, not all columns might contain data.
The first five columns describe the region itself. Indicating the chromosome it is on, the base pair start and end position, number of probes present in the region and the cytoband(s) it covers.
All columns thereafter are sample-specific. The prefix of each column describes what kind of data it contains:
- chip; Log2 ratio of the measurement
- flag; Copy number state of the region. -2 (homozygous loss), -1 (loss) 0, (normal), 1 (gain), 2 (amplification)
- probhomloss; Probability of homozygous loss
- probloss; Probability of loss
- probnorm; Probability of normal
- probgain; Probability of gain
- probamp; Probability of amplification
Note: when opening the file as a spreadsheet, the header is shifted one column to the right of its corresponding data values.
json representation of the jobInfo.txt
A file with two columns: PATIENT_NUM and GROUP. The PATIENT_NUM shows the subject identifiers and the group column describes to which group each subject belongs.
An image file with one plot per group. Depending on the selected input data either produces a simple frequency plot or a frequency plot using qDNAseq. The simple frequency plot is used when there is overlap in the regions/genes selected, when there is no overlapping data the qDNAseq plotting is used.
Simple frequency plot:
- X-axis shows the chromosomes where the size of the chromosomes is determined by the number of probes used to measure the data. The X-axis label indicates that it shows the “chromosome (number of probes)”.
- The left-hand Y-axis shows the frequency of gains and losses, the right-hand side shows the False Discovery Rate (FDR) which is not plotted.
- The X-axis shows chromosomes where the size of the chromosomes are determined by the number of base pairs in the chromosomes. The X-axis label indicates that is shows “chromosome (base pairs)”.
- The Y-axis shows the frequency of gains and losses.
- In the top left corner the number of bins and used bin size in kilo basepairs (kbp) are displayed.
- In the top right corner the number of samples for which the data was plotted is shown.