User: gv

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gv40
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13 hours ago
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5 years, 7 months ago
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Posts by gv

<prev • 26 results • page 1 of 3 • next >
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model matrix in limma
... Hi, I am trying to build a model matrix in limma to perform differential analysis of my features. I have a simple phenodata like this: Sample condition dmso_1 control dmso_2 control dmso_3 control pi3_1 drug pi3_2 drug pi3_3 drug I want to see differential changes 2 con ...
limma R written 20 hours ago by gv40 • updated 18 hours ago by Gordon Smyth39k
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Comment: C: Comparing factor levels in deseq2
... Hi Michael, I read the examples, I am getting this as my output to `resultsNames(ddsMat)` "Intercept" "condition_A_1_vs_A_2" "condition_B_2_vs_A_2" "condition_B_1_vs_A_2" Do I need to use contrast in a list fashion, something like this to capture(A1+A2) vs (B1+B2) `con ...
written 7 days ago by gv40
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Comparing factor levels in deseq2
... Hi, I have sample information (sampleinfo) in this format: SampleID condition type MP_1 A_1 Paired-End MP_2 A_1 Paired-End MP_3 A_1 Paired-End MN_1 A_2 Paired-End MN_2 A_2 Paired-End MN_3 A_2 Paired-End WP_1 B_1 Paired-End WP_2 B_1 Paired-End WP_3 B_1 Paired ...
deseq2 written 7 days ago by gv40
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Comment: C: null model and DEXSeqDataSet object in DEXSEQ
... Thanks a lot Alejandro for making it clear. Regarding making DEXSeqDataSet, my alternativeCountData which is a count matrix of GENES in my case should have same number of rows as my initial count matrix(which is junction counts)? And the names of the rows should be the same in 2 count matrix? ...
written 7 months ago by gv40
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null model and DEXSeqDataSet object in DEXSEQ
... Hi Alejandro and Michael, Thanks a lot for helping me out with DEXSEQ package. I have some questions regarding it: Ques1. I was reading DEXSEQ.pdf and the explanation of null model ( ∼ sample + exon ) vs alt model (∼ sample + exon + condition:exon) Under null model, what is the hypothesis? I ...
dexseq deseq2 written 7 months ago by gv40
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Comment: C: estimateDispersions calculation for > 500,000 exons for 2 conditions taking fore
... Hi Alenjandro, I have edited the post with my sessionInfo(). My program did finish overnight though. It took more than 3 hours I guess. I will try to put in parallel option. Also can you tell me about removing exons which has no counts and it's effect downstream such as in making plots? Thanks a lot ...
written 7 months ago by gv40
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Comment: C: estimateDispersions calculation for > 500,000 exons for 2 conditions taking fore
... HI Michael, Thanks for the reply. I thought that too. But the problem I see in that approach is : What if for a particular gene which has 10 exons, exon1 does not have enough reads(threshold value >10), then this exon according to my filtering will not be present in the initial matrix. Would that ...
written 7 months ago by gv40
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estimateDispersions calculation for > 500,000 exons for 2 conditions taking forever
... I am trying to run DEXSeq package for 2 conditions, control and treatment. This is hg19 genome. I have used python scripts to create the matrix. In the matrix I have >500,000 exons which is typical for human genome. Below is the first 20 lines of my matrix: exon C1A C1B C1C C2A C2B C2C ...
dexseq deseq2 written 7 months ago by gv40
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Comment: C: plotMA in deseq2
... Hi Michael Thanks for the reply. It seems like the default for plotMA is 0.1 from this line plotMA"(object, alpha = 0.1, main = "", xlab = "mean of normalized counts", ylim, MLE = FALSE, ...) Also I am trying to play with lfcThreshold parameter of the results function(will ask a separate question on ...
written 14 months ago by gv40 • updated 14 months ago by Michael Love26k
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plotMA in deseq2
... Hi, In DESeq2, while making  MAPlot for an object obtained by using results function, is there a way to highlight only those genes, whose log2FC values are >= |1|. For example: ddsMat <- DESeq(ddsMat) (res.05_FC0<-results(ddsMat,alpha=0.05,lfcThreshold = 0)) plotMA(res.05_FC0,main="D ...
deseq2 written 14 months ago by gv40 • updated 14 months ago by Michael Love26k

Latest awards to gv

Popular Question 12 months ago, created a question with more than 1,000 views. For ddCt calculation using bioconductor package
Popular Question 12 months ago, created a question with more than 1,000 views. For Microarray data analysis for detecting alternative splicing
Popular Question 12 months ago, created a question with more than 1,000 views. For ddCt calculation using bioconductor package
Popular Question 16 months ago, created a question with more than 1,000 views. For read.celfiles error
Popular Question 2.5 years ago, created a question with more than 1,000 views. For read.celfiles error

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