Hi,

Section 3.3 of the DESeq vignette of the current released version is about
working without any replicates. Perhaps that will sort you out?

http://www.bioconductor.org/packages/release/bioc/vignettes/DESeq/inst/doc/DESeq.pdf

HTH,
Steve

On Saturday, September 15, 2012, Andres Eduardo Rodriguez Cubillos wrote:

> 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
>
> LAMFU
> Universidad de los Andes
> Bogotá D.C.
> Colombia
>


-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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