DESeq do not take variance due to read mapping uncertainty into
consideration. Because read mapping ambiguity is prevalent among
isoforms and de novo assembled transcripts, these tools are not ideal
-for DE detection in such conditions.
-
-**EBSeq**, an empirical Bayesian DE analysis tool developed in
-UW-Madison, can take variance due to read mapping ambiguity into
-consideration by grouping isoforms with parent gene's number of
-isoforms. In addition, it is more robust to outliers. For more
-information about EBSeq (including the paper describing their method),
-please visit <a
+for DE detection in such conditions.
+
+EBSeq, an empirical Bayesian DE analysis tool developed in UW-Madison,
+can take variance due to read mapping ambiguity into consideration by
+grouping isoforms with parent gene's number of isoforms. In addition,
+it is more robust to outliers. For more information about EBSeq
+(including the paper describing their method), please visit <a
href="http://www.biostat.wisc.edu/~ningleng/EBSeq_Package">EBSeq
website</a>.
-RSEM includes the newest version of EBSeq in its folder
-named 'EBSeq'. To use it, first type
+RSEM includes EBSeq in its folder named 'EBSeq'. To use it, first type
make ebseq
NgVec <- scan(file="output_name.ngvec", what=0, sep="\n")
-. After that, replace 'IsoNgTrun' with 'NgVec' in the second line of
-section 3.2.5 (Page 10) of EBSeq's vignette:
+. After that, set "NgVector = NgVec" for your differential expression
+test (either 'EBTest' or 'EBMultiTest').
- IsoEBres=EBTest(Data=IsoMat, NgVector=NgVec, ...)
For users' convenience, RSEM also provides a script
'rsem-generate-data-matrix' to extract input matrix from expression
IsoMat <- data.matrix(read.table(file="output_name.counts.matrix"))
-before running function 'EBTest'.
-
-At last, RSEM provides a R script, 'rsem-find-DE', which run EBSeq for
-you.
-
-Usage:
-
- rsem-find-DE data_matrix_file [--ngvector ngvector_file] number_of_samples_in_condition_1 FDR_rate output_file
-
-This script calls EBSeq to find differentially expressed genes/transcripts in two conditions.
-
-data_matrix_file: m by n matrix containing expected counts, m is the number of transcripts/genes, n is the number of total samples.
-[--ngvector ngvector_file]: optional field. 'ngvector_file' is calculated by 'rsem-generate-ngvector'. Having this field is recommended for transcript data.
-number_of_samples_in_condition_1: the number of samples in condition 1. A condition's samples must be adjacent. The left group of samples are defined as condition 1.
-FDR_rate: false discovery rate.
-output_file: the output file. Three files will be generated: 'output_file', 'output_file.hard_threshold' and 'output_file.all'. The first file reports all DE genes/transcripts using a soft threshold (calculated by crit_func in EBSeq). The second file reports all DE genes/transcripts using a hard threshold (only report if PPEE <= fdr). The third file reports all genes/transcripts. The first file is recommended to be used as DE results because it generally contains more called genes/transcripts.
+before running either 'EBTest' or 'EBMultiTest'.
-The results are written as a matrix with row and column names. The row names are the differentially expressed transcripts'/genes' ids. The column names are 'PPEE', 'PPDE', 'PostFC' and 'RealFC'.
+Lastly, RSEM provides two scripts, 'rsem-run-ebseq' and
+'rsem-control-fdr', to help users find differential expressed
+genes. First, 'rsem-run-ebseq' calls EBSeq to calculate related statistics
+for all genes/transcripts. Run
-PPEE: posterior probability of being equally expressed.
-PPDE: posterior probability of being differentially expressed.
-PostFC: posterior fold change (condition 1 over condition2).
-RealFC: real fold change (condition 1 over condition2).
+ rsem-run-ebseq --help
-To get the above usage information, type
+to get usage information or visit the [rsem-run-ebseq documentation
+page](http://deweylab.biostat.wisc.edu/rsem/rsem-run-ebseq.html). Second,
+'rsem-control-fdr' takes 'rsem-run-ebseq' 's result and reports called
+differentially expressed genes/transcripts by controlling the false
+discovery rate. Run
- rsem-find-DE
+ rsem-control-fdr --help
-Note: any wrong parameter setting will lead 'rsem-find-DE' to output
-usage information and halt.
+to get usage information or visit the [rsem-control-fdr documentation
+page](http://deweylab.biostat.wisc.edu/rsem/rsem-control-fdr.html). These
+two scripts can perform DE analysis on either 2 conditions or multiple
+conditions.
Questions related to EBSeq should
be sent to <a href="mailto:nleng@wisc.edu">Ning Leng</a>.
projects / rsem.git / blobdiff