'rsem-run-ebseq': Added 'output_file.condmeans' for tests with more than 2 conditions

[rsem.git] / README.md

diff --git a/README.md b/README.md
index 4b0b3ec6bbea187f13a41dfeb8fb873aaa3b1d36..f729ef8136adfa47c293ff4d6d0aada39dd30416 100644 (file)
--- a/README.md
+++ b/README.md
@@ -307,19 +307,17 @@ Popular differential expression (DE) analysis tools such as edgeR and
 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. 
+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>.
+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 [EBSeq's
+website](http://www.biostat.wisc.edu/~ningleng/EBSeq_Package).
 
-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
 
@@ -352,10 +350,9 @@ run 'rsem-generate-ngvector' first. Then load the resulting
 
     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
@@ -368,36 +365,32 @@ all isoform level results. You can load the matrix into R by
 
     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: 
+before running either 'EBTest' or 'EBMultiTest'.
 
-    rsem-find-DE data_matrix_file [--ngvector ngvector_file] number_sample_condition1 FDR_rate output_file
+Lastly, RSEM provides two scripts, 'rsem-run-ebseq' and
+'rsem-control-fdr', to help users find differential expressed
+genes/transcripts. First, 'rsem-run-ebseq' calls EBSeq to calculate related statistics
+for all genes/transcripts. Run 
 
-This script calls EBSeq to find differentially expressed genes/transcripts in two conditions.
+    rsem-run-ebseq --help
 
-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_sample_condition1: 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.
+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
 
-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'.
+    rsem-control-fdr --help
 
-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).
+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.
 
-To get the above usage information, type 
-
-    rsem-find-DE
-
-Note: any wrong parameter setting will lead 'rsem-find-DE' to output
-usage information and halt.
+Please note that 'rsem-run-ebseq' and 'rsem-control-fdr' use EBSeq's
+default parameters. For advanced use of EBSeq or information about how
+EBSeq works, please refer to [EBSeq's
+manual](http://www.bioconductor.org/packages/devel/bioc/vignettes/EBSeq/inst/doc/EBSeq_Vignette.pdf).
 
 Questions related to EBSeq should
 be sent to <a href="mailto:nleng@wisc.edu">Ning Leng</a>.
@@ -415,6 +408,8 @@ differential expression analysis.
 
 We thank earonesty for contributing patches.
 
+We thank Han Lin for suggesting possible fixes. 
+
 ## <a name="license"></a> License
 
 RSEM is licensed under the [GNU General Public License