paired differential expression analysis

choosefile   example / example

choosefile   example

choosefile   example

choosefile   example

Function: The experiment designed as samples paired according to the principle of similarity of some important characteristics is calls paired experiment. A pair of samples belong to different groups. Paired t-test is used for paired experiment so that the pair relationship can be taken into consideration when running t-test.


The files input must be txt files. The files can be edited in Excel and saved as txt files.

(1) Different analysis table fileInput a tab delimited text file with headers. The first row is sample names and the first column is variable name. Values in the table are variable value.

(2) Grouping file: Input a tab delimited text file without headers. The first row is sample names and the second row is group names. Samples with same groupe name will be grouped in one group.

(3) Comparison file: Input a tab delimited text file without headers. Two rows are both group names where a row represents a comparison with the second column versus the first column.

(4) Pair file: Input a tab delimited text file with out headers. Rows are all sample names where columns in one row have pair relationship.


Test value: Test value is set to estimate how different two groups are. You can choose P value or Q value for test value. Q value (false discovery rate, FDR) is calculated by FDR correction of P value.

Threshold of test value: The threshold is set to determine whether two groups have significant difference. You can choose P value or Q value as test value.

Threshold of fold change: The threshold is alternatively possessed.

NormFactorsIn RNA-seq, the expression of a gene (RPKM) is measured as the ratio of this gene’s expression and total RNAs’ expression. However, due to the possible difference of total RNA counts between different samples, the estimation of RPKM may lead to error. Hence, edgeR software can use NormFactors to correct this kind of error.


1.diff.stat.xlsstatistical table of differential variable numbers

2.diff.stat.pdf/pngdifferential variable histogram between comparison groups (vector/scalar figure)

3.A-vs-B.all. xlsDifferentially variable values table

4.A-vs-B.filter.xlsSignificantly differentially variable values table

5.A-vs-B.volcano.pdf/pngDifferentially variable values volcano plot (vector/scalar figure)

The file input must be txt format and the data should be separated by separator.


1. Expression file:


2. Group file:


3. Compare file:


4. Pair file:



1. All files output:


2. The table of all genes tested:


3. The table of genes filtered:


4. Volcano figure:


5. The statistics of differential genes: