User: jtremblay514

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Posts by jtremblay514

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Comment: C: edgeR long vectors support when normalizing abundance matrix
... It worked with fwrite (data.table). ...
written 12 months ago by jtremblay5140
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Comment: C: edgeR long vectors support when normalizing abundance matrix
... It is huge I concur and I have to admit that I might have to revisit my SOPs as projects (and datasets) are becoming bigger and bigger. For downstream analyses, only subsets of this final normalized matrix will be pulled (i.e. certain genes with selected functions) at a time, so it shouldn't be a pr ...
written 12 months ago by jtremblay5140
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Comment: C: edgeR long vectors support when normalizing abundance matrix
... I have a 9582472 x 381 matrix. I can share if needed. Thx!   ...
written 12 months ago by jtremblay5140
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Comment: A: edgeR long vectors support when normalizing abundance matrix
... Well it seems I've got another error downstream - here is part of my code:   y <- DGEList(df, remove.zeros=TRUE)   y <- calcNormFactors(y, method="TMM") # Altough not sure if necessary...   cpms = cpm(y)   cpms = round(cpms, digits=3)   write.table(cpms, outfileCpm, quote=FALSE, sep="\t", row ...
written 12 months ago by jtremblay5140
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Comment: A: edgeR long vectors support when normalizing abundance matrix
... Okay it works fine with the devel package. Many thanks! ...
written 12 months ago by jtremblay5140 • updated 12 months ago by Gordon Smyth35k
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Comment: C: edgeR long vectors support when normalizing abundance matrix
... my edgeR version is: edgeR_3.18.1 with R 3.4.0 ...
written 12 months ago by jtremblay5140
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edgeR long vectors support when normalizing abundance matrix
... Dear BioConductor community, I've recently been trying to normalizing large metagenome abundance matrices with the function cpm(y) of edgeR. I get the following error: Error in .isAllZero(counts) :   long vectors not supported yet: memory.c:3438 Calls: mergeTables -> DGEList -> .isAllZero -& ...
edger cpm written 12 months ago by jtremblay5140
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Comment: C: edgeR and gene filtering
... Thanks for the explanation and discussion link it clarifies things.   ...
written 3.0 years ago by jtremblay5140
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edgeR and gene filtering
... Dear Bioconductor community, I'm currently exploring the implementation of edgeR for assessing differential abundance of metagenomics datasets. Briefly, I start with short Illumina reads, assemble them into large contigs. Gene calling is done on these contigs and raw reads are mapped on these genes ...

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