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@arteymix arteymix released this 26 Jun 02:41
· 486 commits to development since this release
1.31.8
352c2f5

Changeset

  • fix various issues with platform and vector merging
  • new endpoint exposing batch information and effect (reserved for curators)
  • quantitation type can be retrieved by name in the REST API
  • improvement for creating and deleting vectors in batch
  • improve serialization of interaction and continuous factors when producing result sets in TSV

Improved encoding of interactions and continuous factors in result sets TSV output

Although rarely used, Gemma's linear model can handle continuous factors. The TSV output not fully supports this.

When we produce a TSV output for a result set, we need to encode three types of contrasts: single factor, interaction of two factors and continuous factors. Those are encoded as follows:

  • contrast_{fv_id}_{key} for a single factor
  • contrast_{fv_id1}_{fv_id2}_{key} for an interaction between two factors
  • contrast_{key} for a continuous factor

where {key} is one of coefficient, log2fc tstat or pvalue.

Gemma is inherently limited to a single continuous factor per result set. If that were to change, we would have to account for this by adjusting the encoding.

Retrieve differential expression results across datasets

The RESTful API has been bumped to 2.8.0 and features a new endpoint for retrieving DE results for a given gene across all datasets, subsets and result sets curated in Gemma.

Results can be filtered at the dataset-level with the usual query and filter parameters and paginated with offset and limit. They can also be filtered by corrected P-value using threshold to reject results with a poor fit for the given gene.

GET /datasets/analyses/differential/results/taxa/human/genes/BRCA1 HTTP/1.1

The endpoint can also be requested to produce a tabular output by passing Accept: text/tab-separated-values.

GET /datasets/analyses/differential/results/taxa/{taxon}/genes/{gene} HTTP/1.1
Accept: text/tab-separated-values

Retrieve raw vectors with quantitation type names

It is now possible to use a name for retrieving vectors for a given experiment.

GET /datasets/{dataset}/data/raw?quantitationType={name}

Common quantitation type name for raw data vectors are:

  • log2cpm
  • counts
  • rpkm
  • rma value
  • value

The first three are used for RNA-Seq data.

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