User: gv

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gv30
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3 years, 6 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 4 months ago by gv30 • updated 4 months 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 5 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 7 months ago by gv30 • updated 7 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 18 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 18 months ago by gv30 • updated 18 months ago by Michael Love14k
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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 2.4 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 2.4 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 2.4 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 2.4 years ago by gv30 • updated 2.4 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 2.4 years ago by gv30

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