User: Gary

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Gary0
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Posts by Gary

<prev • 41 results • page 1 of 5 • next >
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Comment: C: How to change sample names in featureCounts or edgeR
... Thank you so much! ...
written 3 days ago by Gary0
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How to change sample names in featureCounts or edgeR
... Hi, I used STAR, featureCounts, and edgeR for RNA-Seq alignment, quantification, and differentially expressed analysis. Could you teach me how to change sample names, e.g. using Chuong533 instead of Users.gary.Documents.Project.20180429_ZebraFinchColor.20180508_Analysis.featurecounts.Chuong553.bam. ...
edger featurecounts written 3 days ago by Gary0 • updated 3 days ago by Gordon Smyth33k
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Comment: C: How edgeR reads an R List object produced by featureCounts
... Thank you so much. ...
written 7 days ago by Gary0
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How edgeR reads an R List object produced by featureCounts
... Hi, I analyze 20 zebra finch RNA-Seq data, using STAR for alignment, Rsubread-featureCounts for quantification, and edgeR for differentially expressed analysis. However, I don’t know how to run edgeR to read an R List object produced by featureCounts (the detail below). Our study is a three-factor f ...
edger featurecounts written 7 days ago by Gary0 • updated 7 days ago by Gordon Smyth33k
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Comment: C: Could not find function "makeTranscriptDbFromGFF"
... You are right and thank you so much. ...
written 8 months ago by Gary0
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Comment: C: Principal component analysis produced by DiffBind, but PC1 with smaller variatio
... Thanks a lot. May I know the prcomp() parameters DiffBind adopted? More importantly, may I set prcomp() parameters in DiffBind by myself, e.g. scale. = TRUE? I really appreciate your help. ...
written 8 months ago by Gary0
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Could not find function "makeTranscriptDbFromGFF"
... Hi, I use makeTranscriptDbFromGFF in GenomicFeatures to access a mandarin duck genome annotation (.gff file) provided by our cooperators. However, it showed that Error in makeTranscriptDbFromGFF("Mandarin.gff", format = "gff") : could not find function "makeTranscriptDbFromGFF". Please see the deta ...
annotation genomicfeatures gff maketranscriptdbfromgff written 9 months ago by Gary0 • updated 8 months ago by Michael Lawrence10.0k
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Principal component analysis produced by DiffBind, but PC1 with smaller variation than PC2
... Hi, I am not sure whether this question here is proper or not. If it is not, I will remove this post. I have a principal component analysis (PCA) figure below produced by DiffBind. After discussing with my colleagues, we wonder why the variation of Principal Component #1 is smaller than Principal ...
diffbind pca written 9 months ago by Gary0 • updated 9 months ago by Rory Stark2.5k
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Comment: C: How DiffBind run PCA based on peak data?
... I really appreciate your detailed and clear explanation. Gary ...
written 9 months ago by Gary0
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Comment: C: How DiffBind run PCA based on peak data?
... Thanks a lot. May I double check with you? I use macs2 to do peak calling and obtain peaks.narrowPeak (BED6+4 format) files. In this case, the peak scores DiffBind adopted is the 5th column (integer score for display), the 8th column (-log10pvalue), or the 9th column (-log10qvalue) for computing pri ...
written 9 months ago by Gary0

Latest awards to Gary

Popular Question 18 months ago, created a question with more than 1,000 views. For How to run the rpkm function of edgeR
Popular Question 18 months ago, created a question with more than 1,000 views. For DiffBind installation doesn't work

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