User: Alan Smith

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Alan Smith140
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Posts by Alan Smith

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Comment: C: Three factor model matrix, contrasts with interactions - DESeq2 / edgeR
... Hi Mike, I initially started with the "group" method to compare those individual contrasts. But in order to find the interaction effect of the strain and treatment, I attempted the 3 factor design. From the DESeq2 manual and workflows, I "understood" the main effects (which are specific to the refe ...
written 6 months ago by Alan Smith140
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Comment: C: DESeq2 multiple interaction terms 3-factor design
... Mike and Stephen, I have two questions on this post (hope you would look at my comment on this very old post) Mike, I have similar experimental design and sorry I'm still confused about your explanation to the third question. Did you mean that we would have to use a different design formula to fin ...
written 6 months ago by Alan Smith140
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Three factor model matrix, contrasts with interactions - DESeq2 / edgeR
... Hello, I'm working on differential expression analysis with the given sample data using DESeq2. Strain=rep(rep(c("ST1","BT6","MT3","XT7"),each=3),4) Treatment=rep(c("Low","High"),each=24,1) Tissue=rep(c("Lvr","Hrt"),each=12,2) targets<-data.frame(Tissue,Treatment,Strain) rownames(targets)<-p ...
edger deseq2 multifactorial design limma voom written 6 months ago by Alan Smith140 • updated 6 months ago by Michael Love14k
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Comment: C: Finding nearest neighbors of given hub gene in a co-expression network module
... That is exactly what I want to do. Thanks a lot Peter.  ...
written 19 months ago by Alan Smith140
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Finding nearest neighbors of given hub gene in a co-expression network module
... Dear Bioconductor Community, I performed signed co-expression network analysis using WGCNA and identified key modules and hub genes within. I want to tease apart nearest neighbors of a given hub gene and perform GO and pathway analyses on those. I tried using RBGL package to convert igraph to graph ...
graph rbgl wgcna coexpression hub genes written 19 months ago by Alan Smith140 • updated 19 months ago by Peter Langfelder1.3k
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Comment: C: ggtree - trouble displaying longer label names
... Thanks a lot. It worked.  ...
written 2.2 years ago by Alan Smith140
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ggtree - trouble displaying longer label names
... Hello, Trying ggtree for the first time, it is very impressive. However, I'm having trouble to get longer labels displayed library(ggtree) tree<-read.tree(text="(Organism1.006G249400.1:0.03977,(Organism2.022118m:0.01337,(Organism3.J34265.1:0.00284,Organism4.G02633.1:0.00468)0.51:0.0104):0.0246 ...
ggtree written 2.2 years ago by Alan Smith140 • updated 2.2 years ago by Guangchuang Yu800
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Reduce the redundancy of enriched GO terms
... Hello, I have been using topGO package to find enriched GO terms in DE gene list. Then I would reduce or remove the redundant GO terms using web tool Revigo (http://revigo.irb.hr/). Could someone please point me to a Bioconductor package or a function (if there is one) that I could use to do the sa ...
genesetenrichment go topgo written 2.8 years ago by Alan Smith140 • updated 2.8 years ago by Luo Weijun1.4k
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Comment: C: Binning expression data along with capturing gene identifiers
... Oh !!! Knew that I must be missing something basic. Thanks a bunch Jo. ...
written 2.8 years ago by Alan Smith140
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Binning expression data along with capturing gene identifiers
... Hello, I'm using cut function to bin my expression data (FPKM) to know the distribution of expression in different bins and plot them. However, it won't capture gene identifiers of genes (row names) in different bins. I wonder if there is any function in one of the Bioconductor packages / any code ...
clustering rnaseqdata written 2.8 years ago by Alan Smith140 • updated 2.8 years ago by Johannes Rainer1.0k

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Popular Question 19 months ago, created a question with more than 1,000 views. For Reduce the redundancy of enriched GO terms
Popular Question 19 months ago, created a question with more than 1,000 views. For Reduce the redundancy of enriched GO terms

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