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.
The Alteration Type of the analysis is shown in the aberrationType parameter, which will be either -1 (LOSS), 0 (BOTH) or 1 (GAIN). numberOfPermutations shows the total permutations performed, while statisticsType indicates the test chosen in the Statistical Test option (Chi-square, Wilcoxon or Kruskal-Wallis).
Variables selected: groupVariable and regionVariable show the concept paths of the variables used for grouping and the aCGH region variable, 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
This file reflects all subjects in the selected subset, which have data for the group concept. Some of these patients might not have data for the selected aCGH concept. These patients will not be taken into account for the analysis.
- PATIENT_NUM; Subject identifier
- Group; Which of the selected groups the patient belongs to
The groups-test.txt file contains the same general information about the regions as the outputfile.txt, but instead of sample-specific values it shows the gain/loss frequencies (proportions) for each group used in the analysis.
For each region the p-value column shows the significance of the differences in gain/loss frequency between the groups defined. The FDR column represents the false discovery rate.
The groups-test.png file shows a frequency plot of the chromosomal gains and/or losses for two groups used in the analysis. Note: when there are more than two groups selected, only the first two are shown. If Alteration Type “BOTH” was chosen in the analysis, the gains and losses will be shown in two separate graphs.
Which two groups are being compared is shown on the far left side of the plot on the bottom and top corner. The X-axis shows the chromosomes. On the left Y-axis, the percentage of affected subjects in the group is shown (blue for gains, red for losses). The black line represents the False Discovery Rate (FDR), for which the proportion is shown on the right Y-axis.