NEWS

EBSeq 2.0.0

A new implementation of the core functions EBTest and EBMultiTest, which scales up the computation for big number of conditions to compare.

Fixed a bug in EBTest() which may cause error when performing isoform DE testing 1 sample vs. multiple samples.

Correct typos in GetDEResults help file.
Include an alternative method for normalization. The alternative method is similar to median-by-ratio normalization, but can deal with the cases when all of the genes/isoforms have at least one zero counts (in which case the median-by-ratio normalization will fail). This alternative method is developed for single-cell RNA-seq analysis where the dataset always contains a large amount of zeros.

Fixed a bug which may cause error when input a matrix to the sizeFactors parameter

In EBSeq 1.7.1, EBSeq incorporates a new function GetDEResults() which may be used to obtain a list of transcripts under a target FDR in a two-condition experiment. The results obtained by applying this function with its default setting will be more robust to transcripts with low variance and potential outliers. By using the default settings in this function, the number of genes identified in any given analysis may differ slightly from the previous version (1.7.0 or order). To obtain results that are comparable to results from earlier versions of EBSeq (1.7.0 or older), a user may set Method="classic" in GetDEResults() function, or use the original GetPPMat() function. The GeneDEResults() function also allows a user to modify thresholds to target genes/isoforms with a pre-specified posterior fold change.
Also, in EBSeq 1.7.1, the default settings in EBTest() and EBMultiTest() function will only remove transcripts with all 0's (instead of removing transcripts with 75th quantile less than 10 in version 1.3.3-1.7.0). To obtain a list of transcripts comparable to the results generated by EBSeq version 1.3.3-1.7.0, a user may change Qtrm = 0.75 and QtrmCut = 10 when applying EBTest() or EBMultiTest() function.

An extra numerical approximation step is implemented in EBMultiTest() function to avoid underflow. The underflow is likely due to large number of samples. A bug in EBMultiTest() is fixed. The bug will cause error when there is exactly 1 gene/isoform that needs numerical approximation.

An extra numerical approximation step is implemented in EBTest() function to avoid underflow. The underflow is likely due to large number of samples.

In EBSeq 1.3.3, the default setting of EBTest function will remove low expressed genes (genes whose 75th quantile of normalized counts is less than 10) before identifying DE genes. These two thresholds can be changed in EBTest function. Because low expressed genes are disproportionately noisy, removing these genes prior to downstream analyses can improve model fitting and increase robustness (e.g. by removing outliers).