[BioC] DESeq - Estimating Dispersion with Technical Replicates

Andres Eduardo Rodriguez Cubillos ae.rodriguez230 at uniandes.edu.co
Sat Sep 15 06:14:00 CEST 2012

Good day everyone,

My name is Andrés. I'm from Universidad de los Andes located in Bogota D.C. (Colombia) and am currently using the DESeq package to analyze differential gene expression between two experimental conditions.

I attach an example of the countData format I'm using to run the analysis in DESeq. Each column represents a treatment, or condition, that has the mean counts of two technical replicates; each row represents the FPKMs (count reads) obtained from CuffCompare after our RNA-seq data was processed through Bowtie and Cufflinks.

In our experiment we used a technical replicate for each condition and, according to the user guide provided by Simon Anders, we must sum up their counts to get a single column corresponding to a unique biological replicate. At the end I end up with two columns: each one representing a condition that has the mean counts from the two technical replicates of that condition. It's important to say that we do not have any biological replicates, only technical replicates.

Everything appears to be going fine until we try to estimate the dispersion of the normalized counts... an error message appears indicating that "X must be an array of at least two dimensions". I attach my results and the error message.

I hope you can help us solve this issue. We're thinking this error might be related to the fact that we only have one column for each condition: one for "treated" and one for "untreated". In the countData from the guide I see there's more than one column for each condition: "treated2", "treated3" and "untreated3", "untreated4" (Guide: Analysing RNA-seq Data with the DESeq Package from 2012-03-16). However, if we only want to compare two conditions that only have technical replicates, we can only produce one column per condition because we must sum up both technical replicates into one column.

We'll be glad to hear from you and appreciate any advice you can give us.

Best regards,

Andrés Rodríguez

Universidad de los Andes
Bogotá D.C.
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