User: agustin.gonvi

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Cleveland, OH
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@AgustinGonVi
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1 week, 3 days ago
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Posts by agustin.gonvi

<prev • 9 results • page 1 of 1 • next >
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tximport from Galaxy output
... I am using Galaxy, and the output of both Salmon and Kallisto is an *.tabular file per sample with the following format: > Name Length EffectiveLength TPM NumReads > ENSMUST00000193812.1|ENSMUSG00000102693.1|OTTMUSG00000049935.1|OTTMUST00000127109.1|4933401J01Rik-201|4933401J01Rik|1070|TEC| 1 ...
normalization tximport written 27 days ago by agustin.gonvi10 • updated 27 days ago by Michael Love24k
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Comment: C: How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
... Would it work if you calculate the adjustment coefficients using the controls only and then apply the adjustment to all samples? In that way controls from both databases will be centered and the large biological effect will not affect the adjustment. ...
written 5 weeks ago by agustin.gonvi10
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Comment: C: WGCNA with paired samples
... I’ve read in other posts that a strong driver of gene expression could reduce the number of modules. Trying to put that together with what you just said, I am thinking that in the case of low numbers of modules due to a strong biological relevant driver the modules will still be there, but the algo ...
written 6 weeks ago by agustin.gonvi10
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Comment: C: WGCNA with paired samples
... > I don't see how approach 1 would be useful in answering your question except if you had a hypothesis that the network organization is different pre- and post-training. Is this a crazy idea? I would think that certain genes with low basal expression values and low module membership overall, can ...
written 6 weeks ago by agustin.gonvi10
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Comment: C: Steep dendrograms and few modules. WGCNA on RNA seq data
... Thanks! I've noticed that 3 RNA seq databases I am working with reach a fitting index of 0.8 between 4 and 6 stp. With micro-arrays, I was using numbers stp 9 and 11. That could be the problem. Is there a mean connectivity I should be shooting for? I was working under the assumption that the largest ...
written 6 weeks ago by agustin.gonvi10
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Steep dendrograms and few modules. WGCNA on RNA seq data
... Hi, I am trying to run WGCNA on RNA seq data and I end up with few modules. I've seen a [similar post][1] but unlike those data, mine present a better scale free topology index. I run 3 different databases and always have similar results, I am wondering if I am missing something. [Fitting Index][ ...
wgcna rna seq written 6 weeks ago by agustin.gonvi10 • updated 6 weeks ago by Peter Langfelder2.1k
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Rsubread installation problem
... Hi, I updated today to R version 3.6.0 (2019-04-26) -- "Planting of a Tree" and I am having trouble installing Rsubread. The message in console is bellow. Any suggestion to solve this? Thanks >if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") ...
rsubread biocparallel written 8 weeks ago by agustin.gonvi10 • updated 8 weeks ago by Gordon Smyth37k
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Answer: A: Minimum number of samples per treatment/group for WGCNA analysis
... You need a recommended minimum of 15 samples to build a network using all samples together regardless of treatment. Intuitively I will say that if groups members are evenly distributed is better. On a second step, you will correlate modules with treatments and test for significance, the sample size ...
written 9 weeks ago by agustin.gonvi10
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Consensus modules preservation WGCNA
... Hi, I created a consensus modules from 2 coexpression networks from different transgenic animals, and I would like to see which of those modules are not preserved in wild-type by measuring module preservation between consensus and wt. Is it possible to do this? I am asking because module preserva ...
wgcna networks written 3 months ago by agustin.gonvi10 • updated 3 months ago by Peter Langfelder2.1k

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