DESeq2 for two sample conditions

Question

[Aaliya]

Hello, I am working with two sample conditions: control vs treatment.

My sample space looks like this:

ENA Number File Name condition

SRX4455233 E_C_1 control

SRX4455236 E_A_1 treatment

When i tried running DESeq2 on this, the error pops up:

dds <- DESeq(dds)

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.

What does this mean? How can I work on this? I cannot perform DESeq2 on lesser sample space?

[kuttibiotech2009]

Without replication, we cannot perform DE analysis deseq2. Try edgeR

[Michael]

No, the idea is to use replication.

Answer 1

[Michael]

I think that means that you cannot do DE analysis without replicates. You have only one sample per condition and therefore, dispersion (variation) cannot be estimated. If you are re-analysing existing data from ENA anyway, include more datasets to have at least 3 replicates per condition. Your runs are part of BioProject PRJNA482755 which contains 10 samples. However, this is a miRNA experiment, possibly not the best to practice DESeq analysis on.

[Aaliya]

Hey Michael, I understand what you are saying, and the same thought was running in my mind. I am very new to DESeq, could you explain what you meant by, "this is a miRNA experiment, possibly not the best to practice DESeq analysis on"?

Thanks!