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Recent Replies
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
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sovrappensiero
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90
Ah, yes this makes sense! I knew this was an issue with, say, using kraken2 on shotgun metagenomic reads, but I don't have a lot of experi…
Comment: How to access TCGA samples that were treated with a specific drug?
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Thank you. Maybe it's best to confirm with the authors about how they're getting responder/non-responder labels. I'll do that now.
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
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If you sequenced a short hypervariable region, most of your sequence reads will not be able to be assigned to the species level. One possi…
Comment: anRichment is missing
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Consider emailing Dr. Horvath about this. Until enough people make him aware of this issue WGCNA "problem" is unlikely to get fixed.
Comment: anRichment is missing
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Unfortunately, there are only tutorials and codes for tutorials for WGCNA, not installation files for any their packages... :(
Comment: anRichment is missing
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See this link for the WGCNA documentation and code from Peter Langfelder : https://bioinformatics.stackexchange.com/questions/21885/where-t…
Comment: anRichment is missing
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The problem is back, Horwath's lab web is down again. Is it possible to get anRichment istallation file somewhere? (The greater problem is …
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1. Maribaculaceae is a family not a genus
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the within-group variability is so small that these look like technical replicates rather than independent biological replicates
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No. Homology is defined as shared common ancestry.
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I quickly googled [the source code of that function][1], and the error is triggered by this condition:
if(length(wn) < 1 || !is.whol…
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Thanks for the explanation.
I noticed and corrected a typo in which "*read* reverse strand" initially read as "*mate* reverse strand" in t…
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It's a commercial product, a *Staphylococcus hominis* genome. This species is not found in the DADA2 results, so I guess DADA2 is not ident…
Comment: Question regarding WGCNA
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Plots are incomplete without legends. Please share the complete plot with mappings for shape and color.
Comment: Quetion regarding WGCNA
by
deepak
•
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Thank you for your reply andres.firrincieli. I have attached the PCA plot of the expression data used in the WGCNA.
version 2.3.6
version 2.3.6