Running DESeq2 stats with one control

[Eric Gathirwa]

Hi Sam,

I hope you are well.

I have been doing the DESeq2 analysis with R but I have one control. This flags an error when running the following command:

baseMeanPerLvl <- sapply( levels(dds$condition), function(lvl) rowMeans( 

#  counts(dds,normalized=TRUE)[,dds$condition == lvl] ) )

error: Error in base::rowMeans(x, na.rm = na.rm, dims = dims, ...) : 

    'x' must be an array of at least two dimensions

I have tried to apply my own fixes and these files (whose link I have shared) are what I generate as my final output. Are they what you would expect, or do they have unwanted fields?

Thank you.

Warm regards,

Eric

[Sam Westreich]

Hi Eric,

Unfortunately, DESeq does require at least 2 samples in each group, including the control group, in order to determine within-group versus between-group variation.  

You could certainly take the complete_table that is generated and use this to do a comparison of means of annotations between samples, but you won't be able to calculate p-values from the DESeq2 package without a second control sample.  You can see Michael Love (one of the creators of DESeq)'s answer here: https://support.bioconductor.org/p/95714/

Best,

Sam

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Sam Westreich, PMP, PhD

Microbiome Scientist, DNAnexus, 

http://www.mosaicbiome.com

[Elisa]

Hi Sam and Everyone, has anyone tried forming contigs with their metatranscriptome data?  I think linking small sequences into larger ones could be useful for increasing the accuracy of the annotations and linking metabolic processes to microbial genus/species.  I hope there imight be a straightforward way to incorporate a contig step in the SAMSA2 pipeline.  I am very thankful for your thoughts and advice, Elisa 

[Sam Westreich]

Hey Elisa, 

I'm not sure if folks have tried this before, but there are some tools for assembly that are suitable for metagenomes; metaSPAdes is one (https://github.com/ablab/spades, part of the SPAdes tool).

I've not tried using one of these assembly tools before running the annotation step, but if someone does try it, I'd be interested to hear the results!

Best,

Sam

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