User: andres.firrincieli

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Posts by andres.firrincieli

<prev • 89 results • page 1 of 9 • next >
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Comment: C: Small number of genes, drop in sft fit curve at higher threshold powers. why?
... The fact that the curve reach a plateau an then plunges at higher powers is caused by a drastric drop in the connectivity. This is quite common when you randomly subsample your dataset as the majority of your genes are supposed to have very low connectivity while only few are highly conencted (hub). ...
written 2 days ago by andres.firrincieli480
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Comment: C: What are recommended parameters for removing rRNA from meta[transcript][gen]omic
... perhaps this would help: http://seqanswers.com/forums/showthread.php?t=42776&page=17 Alternatively, you could use [sortmerna][1] [1]: https://github.com/biocore/sortmerna ...
written 4 days ago by andres.firrincieli480
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Answer: C: Consensus WGCNA: soft-threshold power selection
... I do not get the filtering steps 2 and 3. First, unless you have the exact lenght of the transcripts I would not use TPM on meta-transcriptomic data. Second, your transcripts are already scaled by a factor of 1 million (TPM) but then you use `cpm()` on TPM normalized read count to filter out low e ...
written 4 days ago by andres.firrincieli480
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Comment: C: someone's already working with this helpful OrthoANI (OAT command line)
... for f1 in /path/to/genomes_fasta/* do for f2 in /path/to/genomes_fasta/* do java –jar ./OAT_cmd.jar -blastplus_dir /path/to/NCBI/blast_version/bin/ –fasta1 "$f1"-name –fasta2 "$f2" done done I never used orthoANI before so I would try this with few genomes e.g. ...
written 13 days ago by andres.firrincieli480
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Comment: C: someone's already working with this helpful OrthoANI (OAT command line)
... I never used orthoANI but the usage is pretty simple, it is an `all vs all`. What did you try so far? ...
written 13 days ago by andres.firrincieli480
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Comment: C: WGCNA eigengenes and sample number reduction
... MEs = moduleEigengenes(datExpr, moduleColors)$eigengenes #calculate module eigengenes (ME) moduleTraitCor = cor(MEs, datTraits, use = "p") # correlate MEs to the experimental variables nSamples = nrow(datExpr) # get the number of samples in datExpr moduleTraitPvalue = corPvalueStuden ...
written 14 days ago by andres.firrincieli480
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Comment: C: WGCNA eigengenes and sample number reduction
... Hi, from the tutorial I was not able to replicate the error so I guess you missed some step. I can not resolve it. You could create a new post ...
written 17 days ago by andres.firrincieli480
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Comment: C: WGCNA eigengenes and sample number reduction
... there is a problem with datExpr. Your matrix is not numeric. Are you following the tutorial? ...
written 18 days ago by andres.firrincieli480
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Comment: C: WGCNA eigengenes and sample number reduction
... Unfortunately no. I usually detect the interesting modules by correlating the 1st PC with my experimental variables. Once I found the 'interesting' modules, I perform an enrichment analysis, and then look at the hubs genes to verify if the highly connected genes are part of the enriched terms (KEGG ...
written 23 days ago by andres.firrincieli480
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Comment: C: WGCNA eigengenes and sample number reduction
... Yes, it is. Does it look wrong for you? ...
written 24 days ago by andres.firrincieli480

Latest awards to andres.firrincieli

Scholar 4 weeks ago, created an answer that has been accepted. For A: Correlating WGCNA modules to Diseased/Not-Diseased Trait
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: WGCNA gene clusters vs eigengenes
Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: Non-computational challenges in bioinformatics
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Why does my TOM network heatmap for WGCNA display red background and golden modu
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: WGCNA gene clusters vs eigengenes
Scholar 6 months ago, created an answer that has been accepted. For A: Why does my TOM network heatmap for WGCNA display red background and golden modu
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Why does my TOM network heatmap for WGCNA display red background and golden modu
Scholar 7 months ago, created an answer that has been accepted. For A: Why does my TOM network heatmap for WGCNA display red background and golden modu
Scholar 7 months ago, created an answer that has been accepted. For A: Why does my TOM network heatmap for WGCNA display red background and golden modu
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Why does my TOM network heatmap for WGCNA display red background and golden modu

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