---
name: "estimateDE"
section: "1"
platform: "linux"
package: "bitseq"
version: "0.7.5+dfsg-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/estimateDE"
---

# estimateDE(1)

this bitseq module estimates differential expression from data sets

## NAME

estimateDE - this bitseq module estimates differential expression from data sets

## SYNOPSIS

**estimateDE** *-o \<outFilePrefix\> -p \<parFileName\>*  \[*OPTIONS*\] \[*sampleFiles*\]

## DESCRIPTION

Estimate differential expression from the dataset.

-

  \[sampleFiles\] should contain transposed MCMC samples from replicates. To distinguish conditions use C between them e.g.:

-

  samplesC1-R1.rpkm samplesC1-R2.rpkm C samplesC2-R1.rpkm samplesC2-R2.rpkm

## OPTIONS

**--help**

-

  Show this help information.

**--confidenceInterval=**\<cf\>

-

  Percentage for confidence intervals. (default: 95)

**-l** \<lambda0\> ,   **--lambda0=**\<lambda0\>

-

  Parameter lambda\_0. (default: 2)

**--norm=**\<normalization\>

-

  Normalization constants for each input file provided as comma separated list of doubles (e.g. 1.0017,1.0,0.9999 ).

**-o** \<outFilePrefix\> ,   **--outPrefix=**\<outFilePrefix\>

-

  Prefix for the output files.

**-p** \<parFileName\> ,   **--parameters=**\<parFileName\>

-

  File containing estimated hyperparameters.

**-s** ,   **--samples**

-

  Produce samples of condition mean expression apart from PPLR and confidence. (default: Off)

**--seed=**\<seed\>

-

  Random initialization seed.

**-v** ,   **--verbose**

-

  Verbose output. (default: Off)