User: veljokisand

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Posts by veljokisand

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Comment: C: DESeq2 estimateSizeFactors controlGenes return an error
... Yes, rownames(dds) lists all gene names including "spike_gene1" without any problems... ...
written 2 days ago by veljokisand0
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Comment: C: DESeq2 estimateSizeFactors controlGenes return an error
... Sure, we have 4 for our environmental metatranscriptomes, a bit hard to work with 20 or more in this case, they have to be synthetic. Still the final question, I did manage to figure out how to use gene names: dds <- estimateSizeFactors(dds, controlGenes = "spike_gene1") nor dds <- estimate ...
written 5 days ago by veljokisand0
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Comment: C: DESeq2 estimateSizeFactors controlGenes return an error
... ThanksMichael! ok I understood it completely wrong, somehow did not understand that it means matrix index. Just to double check, in genes, matrix my spike in gene is at column 20, I need to specify it as following: dds <- estimateSizeFactors(dds, controlGenes = 20) Veljo   ...
written 6 days ago by veljokisand0
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DESeq2 estimateSizeFactors controlGenes return an error
... Hi, I tried to find in web first but apparently no right answer: I run: dds <- estimateSizeFactors(dds, controlGenes = contGenes) contGenes is a vector but an error message is "Error in counts[controlGenes, , drop = FALSE] : subscript out of bounds" contGenes int values are quite high, and s ...
deseq2 written 7 days ago by veljokisand0 • updated 7 days ago by Michael Love15k

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