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aoles / DEFormats

:recycle: Differential gene expression data formats converter
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conversion list to obj -error #6

Open noor-albader opened 6 years ago

noor-albader commented 6 years ago

Hi I was trying to covert my matrix of normalized results post DESeq2 pipeline back to a DESeq object: (A) First I ran DESeq and normalization to result to a matrix (abund): dds = phyloseq_to_deseq2(ps_time1, ~treatement) ps_dds_tmp <- estimateSizeFactors(dds_2, type = "poscounts") ps_dds_tmp <- estimateDispersions(ps_dds_tmp) abund <- getVarianceStabilizedData(ps_dds_tmp) abund <- abund + abs(min(abund)) (B) Then transformed my matrix (abund) to a DGEList: dge = DGEList(abund, group = group) #this worked fine

class(dge) [1] "DGEList" attr(,"package") [1] "edgeR" (C) But then when I tried to transform it to a DGE obj I get the following error: test = as.DESeqDataSet(dge) Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are not integers

I know they aren't integers because of the normalization but I am ultimately trying to get a DGE obj to run DESeq2's results function to get log2FC, p-values ect.

Any help would be greatly appreciated:)

aoles commented 6 years ago

Thank you for reaching out. Could you maybe share a minimal working example along with sample data which would allow me to reproduce the issue?

I'm not sure though I understand why you would want to convert the normalized data matrix to DGEList and then back to DESeqDataSet? Can't the desired values be directly extracted from the final ps_dds_tmp object?

Cheers, Andrzej