| allcnv |
3 |
Segmentation files containing both germline and somatic CNVs (opposite tag: nocnv). From Broad Institute CNV analyses |
| alleleSpecificCN |
2 |
Allele-specific copy number array signal intensity data for TCGA-LAML. From Washington University St. Louis. |
| B_Allele_Freq |
2 |
The proportion of total signal intensity that is produced by the B allele in a SNP array. Used for TCGA-OV, GBM, LUSC projects (TCGA Analysis of Allele Specific Copy Number). |
| BioSizing |
1 |
Tab-delimited bioanalysis data for calculating fragment size and concentration. |
| byallele |
2 |
Copy number array intensity values calculated in an allele-specific manner. From Broad Institute CNV analyses. See alleleSpecificCN for TCGA-LAML. TCGA level 2 data. |
| cgh |
1 |
Comparative genome hybridization QC data. Available as JPGs (actual photographs of microarray intensities) and PDFs (microarray reports). Subset of tag: qc. |
| cnv |
2 |
Includes copy number variation files measured using CGH array and WGS with Illumina. |
| Delta_B_Allele_Freq |
2 |
The absolute value of the difference between the SNP array B allele frequency in a tumor and its paired normal sample. Used for TCGA-OV, GBM, LUSC projects (TCGA Analysis of Allele Specific Copy Number). |
| Genotypes |
2 |
Information on SNP array calls in A/B format. Available for TCGA-OV, GBM, LUSC projects (TCGA Analysis of Allele Specific Copy Number). |
| hg18 |
3 |
Copy number segmentation files that use hg18 build probes |
| hg19 |
3 |
Copy number segmentation files that use hg19 build probes |
| ismpolish |
2 |
Intensities that have been normalized first using quantile normalization and then by median-polishing. From Broad Institute CNV analyses. Synonymous with Data Type: Normalized copy numbers. TCGA level 2 data. |
| LOH |
3 |
Results from the CBS analysis of the delta B allele frequency data for each tumor/ normal pair. Used for TCGA-OV, GBM, LUSC projects (TCGA Analysis of Allele Specific Copy Number). |
| lowess_normalized_smoothed |
1 |
Log ratio microarray graph, locally weighted scatterplot smoothing. Available as PNG photos for projects TCGA-OV, GBM, LUSC. |
| nocnv |
3 |
Segmentation file only containing somatic CNVs (opposite tag: allcnv). From Broad Institute CNV analyses. |
| Normal_LogR |
2 |
Log2 of the total signal intensity of a normal sample to reference genome ratio. Used for TCGA-OV, GBM, LUSC projects (TCGA Analysis of Allele Specific Copy Number). |
| Paired_LogR |
2 |
Log2 of the total signal intensity for a tumor to its paired normal sample ratio. Used for TCGA-OV, GBM, LUSC projects (TCGA Analysis of Allele Specific Copy Number). |
| pairedcn |
2 |
Tumor-normal paired copy number variation array intensity files for TCGA-LAML. From Washington University St. Louis. |
| QA |
1 |
Case-level QA metrics for microarray data. Used for TCGA-OV, GBM, LUSC projects. |
| qc |
1 |
QC data for microarrays. Available as JPGs (actual photographs of microarray intensities) and PDFs (microarray reports) for CGH array data. Available as XML coordinate files and project-level CSVs that contain aliquot fluorescence conjugation levels. |
| raw |
2 |
Copy number value estimations calculated by summing allele-specific values. From Broad Institute CNV analyses. TCGA level 2 data. |
| seg |
3 |
Contains results for copy number segmentation. Used for TCGA-OV, GBM, LUSC projects (TCGA Analysis of Allele Specific Copy Number). |
| segmentation |
2 |
Copy number variation segmentation files measured using Illumina WGS. Contrast with CNV measured with array data files. |
| segmented |
3 |
Segmentation files for TCGA-LAML array data. From Washington University St. Louis. TCGA level 3 data. |
| segnormal |
3 |
Contains segmented log2 ratio data from normal samples. Used for TCGA-OV, GBM, LUSC projects (TCGA Analysis of Allele Specific Copy Number). |
| sif |
2 |
Simple interaction format files. Synonymous with filter "Data Format: SIF" |
| tangent |
2 |
Copy number values calculated with tangent normalization using BirdSuite. Note that these files are used for GDC Data Portal harmonization. TCGA level 2 data. |
| Unpaired_LogR |
2 |
Tumor sample compared to reference pool of normal samples. Used for TCGA-OV, GBM projects (TCGA Analysis of Allele Specific Copy Number). |