User: Sridhara Gupta Kunjeti

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Posts by Sridhara Gupta Kunjeti

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Answer: A: edgeR - multiple comparisions
... Hello Davis, Thank you very much for your comments. I read the documentation, but could not catch this. But with your comments, now it is clear to me. Many thanks, Sridhara On Tue, May 31, 2011 at 7:26 PM, Davis McCarthy wrote: > Hi Sridhara > > The function exactTest() has an argument ...
written 6.5 years ago by Sridhara Gupta Kunjeti320
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Comment: C: edgeR - multiple comparisions
... Hello Davis, Yes, this helped me to solve the problem. On the other hand, I have a different kind of question, which is related to the exactTest. First two columns in my inputs files are the counts for the control group. ============================================= example 1: Textfile1 Gene con ...
written 6.5 years ago by Sridhara Gupta Kunjeti320
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error message in edgeR
... Hi, I got an below error message while running the edgeR. > d10 <- estimateTagwiseDisp(d10, prior.n = 10, grid.length = 500) Using grid search to estimate tagwise dispersion. > prior.n10 <- estimateSmoothing(d10) Warning message: In .odls(scores.g = scores, info.g = exp.inf) : Estimat ...
edger written 6.5 years ago by Sridhara Gupta Kunjeti320 • updated 6.5 years ago by Gordon Smyth32k
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Comment: C: edgeR - multiple comparisions
... Hello Davis, Thank you very much for your email. After looking at one of my comparisons, it makes total sense about the p-value. But, I did notice that out of 10827 genes, most of them (10820) had an *FDR* of 1 and rest others had an FDR of 0.5, 0.6, 0.7, and 0.8 so on.... I was wondering if "0" in ...
written 6.5 years ago by Sridhara Gupta Kunjeti320
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Comment: C: edgeR - multiple comparisions
... Hello Mark, Thank you very much for you email. It greatly helped me to export the FDR, p-value, logFC and logConc into csv format. I have one real quick question, this is more of statistical question. After exporting the FDR, I started analyzing pair by pair. In the below example, what I noticed is ...
written 6.5 years ago by Sridhara Gupta Kunjeti320
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Comment: C: edgeR - multiple comparisions
... Hello Mark, Thanks for your email. I have one quick question. Is it possible to export all the 10,427 genes after passing exactTest()? what argument do I need to use to do that? Basically I wanted the complete list of genes with the following info: > topTags(de06.tgw, n = 10, adjust.method="BH", ...
written 6.5 years ago by Sridhara Gupta Kunjeti320
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edgeR - multiple comparisions
... Hello, I have used edgeR for DGE analysis and I have few questions regarding the model and comparisions. 1) What kind of statistical model is taken into account to analyze treatment structure and conduct analysis of variance? 2) How does the edgeR correct the multiple comparisions? 3) I am assuming ...
edger written 6.5 years ago by Sridhara Gupta Kunjeti320 • updated 6.5 years ago by Mark Robinson1.1k
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Comment: C: edgeR- plotSmear
... Hello Davis, I tried using 'de.tgw' instead of 'd' and I got the following error message: > de <- as.logical(abs(decideTestsDGE(de.tgw))) > plotsymbols <- rep(19, nrow(de.tgw)) > plotsymbols[de] <- 4 > plotSmear(de.tgw, cex = 0.8, main="MM Plot", pch=plotsymbols) Error in plotS ...
written 6.6 years ago by Sridhara Gupta Kunjeti320
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Answer: A: edgeR- plotSmear
... Hello Davis, Here is the history of the codes: d <- DGEList(counts = d, group = group) d d <- estimateCommonDisp(d) d <- estimateTagwiseDisp(d, prior.n = 10, grid.length = 500) prior.n <- estimateSmoothing(d) prior.n de.tgw <- exactTest(d, common.disp = FALSE) de.tgw sum(de.tgw$table ...
written 6.6 years ago by Sridhara Gupta Kunjeti320
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edgeR- plotSmear
... Hello, I have used edgeR for DGE analysis and also generated plotSmear. I guess by dufault the plotSmear shows red dots for differentially expressed genes. But, I want to generate a black and white plot, is there a possbility to gene using different shape of the points, may be 'x' for the differenti ...
edger written 6.6 years ago by Sridhara Gupta Kunjeti320 • updated 6.6 years ago by Davis McCarthy260

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