User: gv

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gv40
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Posts by gv

<prev • 23 results • page 1 of 3 • next >
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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 10 weeks 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 10 weeks 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 10 weeks 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 10 weeks 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 10 weeks 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 9 months ago by gv40 • updated 9 months ago by Michael Love24k
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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 9 months ago by gv40 • updated 9 months ago by Michael Love24k
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(Closed) p-value using moderated t test
... Hi, I have an input file which looks like this: Junctions s1_1 s1_2 s2_1 s2_2 junc1 0.23 0.25 0.76 0.78 junc2 0.27 0.31 0.51 0.50 junc3 0.9 0.78 0.16 0.12 Column1 are the junction coordinates. Column 2 and 3 represent percent splice in(psi) values ...
limma R fdr p-value written 11 months ago by gv40
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Plotting coverage from bam files
... Hi,   I have 4 bam files and a coordinate file in bed format. I want to plot all 4 bam files in one graph for each coordinate I have, and look for differences in coverage across the samples. How can I do this from Bioconductor packages? Thanks   ...
bam plot written 14 months ago by gv40 • updated 14 months ago by James W. MacDonald50k
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pca plot for tissues and protein values
... Hi Everyone,   I want to do a PCA plot for my data frame. Following is the description of my data frame which looks like this: Tissue p1 p2 p3 p4 p5 t1 10.90 0.07 40.57 76.71 12.73 t2 13.57 3.48 27.93 75.46 19.59 t3 1.05 0.04 16.18 8.92 ...
pca written 2.1 years ago by gv40 • updated 2.1 years ago by James W. MacDonald50k

Latest awards to gv

Popular Question 7 months ago, created a question with more than 1,000 views. For ddCt calculation using bioconductor package
Popular Question 7 months ago, created a question with more than 1,000 views. For Microarray data analysis for detecting alternative splicing
Popular Question 7 months ago, created a question with more than 1,000 views. For ddCt calculation using bioconductor package
Popular Question 11 months ago, created a question with more than 1,000 views. For read.celfiles error
Popular Question 2.1 years ago, created a question with more than 1,000 views. For read.celfiles error

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