User: gv

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gv30
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3 years, 4 months ago
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Posts by gv

<prev • 14 results • page 1 of 2 • next >
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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 12 weeks ago by gv30 • updated 12 weeks ago by James W. MacDonald44k
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DEXSeq : for differential exon usage
... Hi, I am trying you use DEXSeq package for differential exon usage. I am interested in only a single exon(hence single gene) to see how differently it is used under different conditions. I created the gff file for only that gene having the exon I am interested in.   Is it fine to run DEXSeq for o ...
dexseq R written 3 months ago by gv30
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Making a gff file for introns to be used with DEXSEQ
... Hi Everyone, I am trying to use DEXSeq to find out intron retention events in my RNA seq data. I want to find first the counts associated with the introns. I made a test gff file and used dexseq_count.py script but it did not produce any counts for introns. Here is how my test.gff file for intron l ...
dexseq written 5 months ago by gv30 • updated 5 months ago by Hervé Pagès ♦♦ 12k
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Comment: C: deseq2 estimating size factors
... Hi Michael Thanks for your reply. I found what i was looking for. Also how can i know which functions can be applied on CLASS DESeqDataSet? For example estimateSizefactors(dds), what else?? Thanks ...
written 16 months ago by gv30
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deseq2 estimating size factors
... Hi Everyone, I am trying to run DESeq2 package in R. After running the package I have few questions. I will start with this. baseMean : It is defines as average of the normalized count values, dividing by size factors, taken over all samples in the DESeqDataSet After this step of the analysis, ...
deseq2 R written 16 months ago by gv30 • updated 16 months ago by Michael Love13k
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Comment: C: DESeq2 rna seq analysis
... @Steve: So I looked at plotCounts function and plotted it for some genes. What should I look for in them so as to distinguish outliers from other differentially expressed gene. ...
written 2.2 years ago by gv30
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Comment: C: DESeq2 rna seq analysis
... Ok I will look at the plotCounts function, it's usage and get back to you. Yes I was referring to the object generated after applying results function res<-results(dds) res<-res[order(res$padj),] ...
written 2.2 years ago by gv30
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Comment: C: DESeq2 rna seq analysis
... So in the file, how can i distinguish red points with red triangles which are outliers?? THis is because I need to know which genes are really differentially expressed and is not an outlier ...
written 2.2 years ago by gv30
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DESeq2 rna seq analysis
... Hi, I am trying to use DESeq2 package. I have some question's related to that. 1. DESeq2 manual say's in MAplot function  Points will be colored red if the adjusted p value is less than 0.1. Can i change the value to 0.05. If yes how?? 2. Also point which falls out of the window are plotted as op ...
deseq2 written 2.2 years ago by gv30 • updated 2.2 years ago by Steve Lianoglou12k
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unable to find an inherited method for function ‘Rle’ for signature ‘"NULL", "missing"
... Hi Everyone, I am trying to run this package called NAGNAG(https://sourceforge.net/projects/nagnag/files) But in one of the commands when I run, I get this error: Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘Rle’ for signature ‘"NULL", "missing" ...
R written 2.2 years ago by gv30

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