User: pjgalli2

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pjgalli20
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Posts by pjgalli2

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Comment: C: Analyzing a continuous phenotype using DESeq2
... Nevermind.  I had the phenotype coded as factors instead of numeric.  Looks like it's working. ...
written 3.3 years ago by pjgalli20
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Analyzing a continuous phenotype using DESeq2
... Hello.  Is it possible to analyze a continuous phenotype with DESeq2, without grouping into factors?  I receive this note when I run the default DESeq function: -- note: fitType='parametric', but the dispersion trend was not well captured by the function: y = a/x + b, and a local regression fit ...
deseq2 continuous written 3.3 years ago by pjgalli20
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Answer: A: metagenomeSeq for continuous phenotype
... Just posted it here: https://github.com/HCBravoLab/metagenomeSeq/issues/36 ...
written 3.3 years ago by pjgalli20
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metagenomeSeq for continuous phenotype
... Hello.  I am trying to run the fitFeatureModel function in metagenomeSeq for a continuous phenotype, but I receive this error: Error in limma::squeezeVar(fit[-exclude, "s2"], fit[-exclude, "df"]) : var is empty Is there a way to use metagenomeSeq for a continuous phenotype?  Thank you. ...
limma metagenomeseq continuous written 3.3 years ago by pjgalli20
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Analyzing microbiome data (many zero-counts) using DESeq2
... I am trying to analyze microbiome data, which is count data with many zero-counts.  I receive this error when I run the DESeq function in DESeq2: estimating size factors Error in estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc, : every gene contains at least one zero, cannot c ...
microbiome deseq2 zero-inflated written 3.3 years ago by pjgalli20 • updated 3.3 years ago by Michael Love25k

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