NEWS.md
In statOmics/satuRn: Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications

1.7.3

Included two additional vignettes to guide users on using satuRn for performing differential usage analyses for (1) exons and (2) equivalence classes.

1.7.2

Minor enhancement for handling fitErrors. When a glm model cannot be fitted, e.g., due to the sparsity of the data, satuRn will record this as a "fitError", returning NA estimates and p-values. However, in extreme cases, e.g., when a feature is not expressed in any sample or cell, the testDTU could fail in older versions of satuRn. With the enhancement in version 1.7.1, such features will be handled correctly, i.e., flagged as fitErrors and assigned NA estimates and p-values. Note that ideally such features should have been removed previously during feature-level filtering.

1.7.1

Attempt to make an enhancement for handling fitErrors. However, this attempt turned out to be unsuccessful, as per GitHub issue 25. Thus, the enhancement was finalised in satuRn version 1.7.2.

1.4.1

We report a bug in satuRn 1.4.0. (Bioconductor release 3.15). The bug was inadvertently introduced in satuRn 1.3.1 (from the former Bioconductor devel). Note that the bug was not thus present in any of the older Bioconductor releases 3.13 and 3.14 (satuRn 1.0.x, 1.1.x and 1.2.x).

Bug details:

Imagine a gene with three isoforms and two cell types. The goal is to assess DTU between cell types. All isoforms are expressed in all cells of cell type 1. However, none of the isoforms are expressed in any of the cells in cell type 2 (i.e., the gene is not expressed in cell type 2).

satuRn computes the log-odds of picking a certain isoform from the pool of isoforms in each cell type, and then compares these log-odds estimates between the cell types. However, in this example, the log-odds of picking a certain isoform from the pool of isoforms in cell type 2 cannot be computed, as there is no data. Hence, the DTU test statistic should be NA. However, due to erroneous handling of NA estimates, which was inadvertently introduced in satuRn 1.3.1. while aiming to resolve github issue 16, the log-odds in cell type 1 will be compared to zero. Hence, (erroneous) results can be obtained for this contrast, even when there are no data in cell type 2.

Note that in many cases such isoforms may not pass filtering and would not get evaluated altogether. However, when analyzing sprase scRNA-Seq datasets with a lenient filtering criterium, this problem will apply, and will result in mistakes in the inference.

satuRn 1.4.0

satuRn version for Bioconductor release 3.15

satuRn 1.3.1

Bug fix: allow for fit errors to be propagated as NA results (github issue 15 by @jgilis)
Bug fix: handle experimental designs with empty factor levels correctly (github issue 16 by @XueyiDong)
Bug fix: identify transcripts that are the only expressed transcript of a gene and set NA results (github issue 17 by @jgilis)
Bug fix: handle extreme z-scores in testDTU with diagplot2 option
Enhancement: plotDTU now allows for sparseMatrix input