User: sebastiano.curreli

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Posts by sebastiano.curreli

<prev • 12 results • page 1 of 2 • next >
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Answer: A: Calculate correlation matrix for gene expression data
... Hi Luan, regarding your analysis I'd suggest you to check out the following R packages: PCA-->FactoMineR: http://factominer.free.fr/classical-methods/principal-components-analysis.html Correlation analysis-->rcorr:  https://www.rdocumentation.org/packages/Hmisc/versions/4.0-2/topics/rcorr ...
written 10 months ago by sebastiano.curreli0
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Comment: C: Plot differential gene expression over genomic coordinates
... Dear Michael,  thank you for your prompt reply. Yes, I'm familiar with the example in your workflow, and so far I've found it really helpful. However, in my case the non-trivial part, is to generate a plot which displaying data coming mapped on different chromosomes.  I'm working on a way around ...
written 10 months ago by sebastiano.curreli0
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Plot differential gene expression over genomic coordinates
... Dear Community, I'm trying to plot the changes in gene expression due to two treatments (compared to a common baseline control) across the mouse genome space. The way I'm envisioning the resulting graph output is the following: - x axis indicating the genomic coordinates (i.e. the ordered chromos ...
gviz written 10 months ago by sebastiano.curreli0 • updated 10 months ago by Michael Love16k
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Comment: C: Using contrast argument of DESeq2 to estimate linear combination coefficients
... Thank you Michael. Your formulation describes somehow what I'm looking for, the problem is that the "distance" I'm willing to use is the number of DE transcripts identified with DESeq2.  I thought to write a function which iterates n times the results extraction while modifying the contrast defini ...
written 12 months ago by sebastiano.curreli0
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Using contrast argument of DESeq2 to estimate linear combination coefficients
... Dear Community,  I'm characterizing transcriptional responses to transcription factors (TFs) overexpression using RNA-seq. In brief, I have 5 groups of samples (x, y, z, xyz, Ctrl), where I provide either x, y or z TFs individually, or simultaneously using a multicistronic vector (xyz); Ctrl repre ...
deseq2 contrast written 12 months ago by sebastiano.curreli0 • updated 12 months ago by Michael Love16k
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Comment: C: Characterization of simultaneous transcription factors over expression
... Thank you Michael, numerator<-c("conditionxyz") denominator<-c("conditionx","conditiony","conditionz") LC<-list(numerator,denominator) DEcomposite<-results(dds, contrast=LC, listValues = c(1,-1/3), alpha=0.05, lfcThreshold = 1, altHypothesis = "greaterAbs", independentFiltering = T) ...
written 19 months ago by sebastiano.curreli0
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Comment: C: Characterization of simultaneous transcription factors over expression
... Dear Ryan, thank you for your reply. You are right, unfortunately I've not been precise in the description of my hypothesis, I apologize for that. Anyway, your suggestions hit exactly the mark. I'm interested in both, first, identifying genes which significantly differ between xyz expression and t ...
written 19 months ago by sebastiano.curreli0
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Characterization of simultaneous transcription factors over expression
...   Dear community, I’m pretty new to computational biology and to transcriptomics. I’m currently trying to characterize how the overexpression of three transcription factors (x, y, z) acts on the transcriptome of a cell line. The design involves 5 groups of samples (x, y, z, xyz, Ctrl), each group ...
deseq2 pca factominer written 19 months ago by sebastiano.curreli0 • updated 19 months ago by Ryan C. Thompson6.3k
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Answer: A: "U" shaped p values distribution in DESeq2 RNA-seq DE analysis using the contras
... Thank you for the clarification Michael! ...
written 21 months ago by sebastiano.curreli0
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"U" shaped p values distribution in DESeq2 RNA-seq DE analysis using the contrast argument
... Dear Community, I'm using DESeq2 to analyze an RNAseq experiement in which I'm evaluating the transcriptional variations mediated by the over expression of some transcription factors. The experimental design is as follows: 5 conditions (ctrl; x; y; z; x+y+z), and each condition ha 5 replicates. I ...

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