User: fernardo

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fernardo 110
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Posts by fernardo

<prev • 46 results • page 1 of 5 • next >
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Is it fine to run SVM on RNA-seq read counts?
... Hi, I have 930 samples of RNA-seq for 4 conditions. I am using RMA processed for the RNA-seq data. Now I am doing the following steps: 1- Picking 75 genes of interest for the 930 samples. 2- Importing such table into SVM to classify those 4 conditions based on those genes. (NOTE: 75% training set ...
svm classification machine learning rna-seq written 8 days ago by fernardo 110 • updated 4 days ago by Charles Warden5.9k
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Comment: C: How to find p-value of the modules in WGCNA?
... well I'd say that I received different clusters (modules) from WGCNA and one of them seems to be more significant based on pathways and so on, not based on the correlation we discussed above. And the genes are all differentially expressed between case/control, so the common pathways across e.g. the ...
written 5 months ago by fernardo 110
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Comment: C: How to find p-value of the modules in WGCNA?
... Not actually. The blue module has not the lowest or the highest number of genes (DEGs). What correlation do you mean? Do you mean using "`summary(lm(CaseControl ~ MEblue))`"? Yes I tried this and were highly significant for almost all the modules. ...
written 9 months ago by fernardo 110
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Comment: C: How to find p-value of the modules in WGCNA?
... Thank you very much, now I have all the answers. But if I may ask about one more interesting point, the blue module has more significant enriched pathways and ontology annotations with even more connection in PPI compared to other modules with low p-value but no enrichment or very less? I can't see ...
written 9 months ago by fernardo 110
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Comment: C: How to find p-value of the modules in WGCNA?
... I changed Y(CaseControl) column to 0 and 1 and worked. But gave a warning message but maybe I can ignore it :) Call: glm(formula = y ~ MEblue, family = binomial(), data = xx) Deviance Residuals: Min 1Q Median 3Q Max -8.106e-05 -2.100e-08 2.100e-08 2. ...
written 9 months ago by fernardo 110
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Comment: C: How to find p-value of the modules in WGCNA?
... Thanks. Understood. Even, unfortunately, it gave an error while I was running CaseControl;y (`summary(glm(y ~ Module1, , data=MyData, family=binomial()))`): Error in eval(expr, envir, enclos) : y values must be 0 <= y <= 1 ...
written 9 months ago by fernardo 110
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Comment: C: How to find p-value of the modules in WGCNA?
... Thank you very much Kevin. I could manage to find the matrix you mentioned between the samples and the modules. But what could be the "**Weight**" or "**CaseControl**"? Thanks ...
written 9 months ago by fernardo 110
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How to find p-value of the modules in WGCNA?
... Hi, I did run **WGCNA** package successfully but I couldn't find a way or line of code to get **p-value** of the **modules**. I have seen it in a paper that there p-value were given to the modules. Can you help please? Thanks a lot ...
wgcna microarray rna-seq R written 9 months ago by fernardo 110 • updated 9 months ago by Kevin Blighe35k
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Comment: C: Differential Gene Analysis
... Can you check how > exprs(gse) and > fac look like? ...
written 10 months ago by fernardo 110
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Comment: C: Why different DEGs between my result and the author's result?
... Well they haven't used Limma but still they provided a table in their paper with "FC (adjusted p <0.0005)" which is clearly the fold change of the genes with that adjusted-p. Mine, had p-value <0.05 but adjusted-p >0.4. ...
written 10 months ago by fernardo 110

Latest awards to fernardo

Popular Question 5 months ago, created a question with more than 1,000 views. For Can ncRNAs be found from all RNA-seq data?
Popular Question 10 months ago, created a question with more than 1,000 views. For Can ncRNAs be found from all RNA-seq data?
Popular Question 22 months ago, created a question with more than 1,000 views. For Why GATK and bcftools SNP calling different?
Student 2.2 years ago, asked a question with at least 3 up-votes. For Why GATK and bcftools SNP calling different?

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