blockmodeling : blockmodeling_0.1.8.tar.gz
R CMD INSTALL -l "." blockmodeling_0.1.8.tar.gz
-EBSeq : blockmodeling EBSeq_1.1.5.tar.gz
- R CMD INSTALL -l "." EBSeq_1.1.5.tar.gz
+EBSeq : blockmodeling EBSeq_1.1.6.tar.gz
+ R CMD INSTALL -l "." EBSeq_1.1.6.tar.gz
rsem-for-ebseq-calculate-clustering-info : calcClusteringInfo.cpp
$(CC) -O3 -Wall calcClusteringInfo.cpp -o $@
Usage:
- rsem-find-DE data_matrix_file [--ngvector ngvector_file] number_sample_condition1 FDR_rate output_file
+ 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_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.
+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.
differential expression analysis.
We thank earonesty for contributing patches.
+
We thank Han Lin for suggesting possible fixes.
## <a name="license"></a> License
+RSEM v1.2.5
+
+- Updated EBSeq from v1.1.5 to v1.1.6
+- Fixed a bug in 'rsem-generate-data-matrix', which can cause 'rsem-find-DE' to crash
+
+--------------------------------------------------------------------------------------------
+
RSEM v1.2.4
- Fixed a bug that leads to poor parallelization performance in Mac OS systems
#!/usr/bin/env Rscript
printUsage <- function() {
- cat("Usage: rsem-find-DE data_matrix_file [--ngvector ngvector_file] number_sample_condition1 FDR_rate output_file\n\n")
+ cat("Usage: rsem-find-DE data_matrix_file [--ngvector ngvector_file] number_of_samples_in_condition_1 FDR_rate output_file\n\n")
cat("This script calls EBSeq to find differentially expressed genes/transcripts in two conditions.\n\n")
cat("data_matrix_file: m by n matrix containing expected counts, m is the number of transcripts/genes, n is the number of total samples.\n")
cat("[--ngvector ngvector_file]: optional field. 'ngvector_file' is calculated by 'rsem-generate-ngvector'. Having this field is recommended for transcript data.\n")
- cat("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.\n")
+ cat("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.\n")
cat("FDR_rate: false discovery rate.\n")
cat("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.\n\n")
cat("The results are written as a matrix with row and column names. The row names are the genes'/transcripts' ids. The column names are 'PPEE', 'PPDE', 'PostFC' and 'RealFC'.\n\n")
while ($line = <INPUT>) {
chomp($line);
my @fields = split(/\t/, $line);
- push(@{$_[2]}, $fields[0]);
+ push(@{$_[2]}, "\"$fields[0]\"");
push(@{$_[1]}, $fields[$offsite]);
}
close(INPUT);
exit(-1);
}
- @ecs = ($ARGV[$i], @ecs);
+ my $colname;
+ if (substr($ARGV[$i], 0, 2) eq "./") { $colname = substr($ARGV[$i], 2); }
+ else { $colname = $ARGV[$i]; }
+ $colname = "\"$colname\"";
+ @ecs = ($colname, @ecs);
push(@matrix, \@ecs);
}