Error of Deseq2

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1

Hello everyone,

I’m currently in the process of performing DEGS idenitification with DESEQ2 in the galaxy pipeline.

I performed all my steps with Galaxy.

I performed whole RNA transcriptome sequencing. The obtained FASTq files I imported into galaxy and then I performed the following steps:

FASTP
FASTQC
HISAT2
STRINGTIE

And I try DESeq2. But few minits later,I got error meassage.I checked “Tool Standard Error” and it says :
estimating size factors
estimating dispersions
Error in checkForExperimentalReplicates(object, modelMatrix) :

The design matrix has the same number of samples and coefficients to fit,
so estimation of dispersion is not possible. Treating samples
as replicates was deprecated in v1.20 and no longer supported since v1.22.

Calls: DESeq … estimateDispersions → .local → checkForExperimentalReplicates

Please give some advices,help me.

2

Hello @hashimoto.takuma

This tool and most other Bioconductor tools require replicates.

FAQ with related tips: Extended Help for Differential Expression Analysis Tools

Give that a review and maybe reorganize your sample data?

If you run into more problems, you can post back the job details and we can try to help more. The part with the inputs and parameters is the most important (“i” icon). Try to leave everything intact with a full copy/paste or screenshot.