User: Gary

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Gary0
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Posts by Gary

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Comment: C: Package is not available for R version 3.5.0
... It is working. Thanks a lot. May I know the difference between biocLite() and install.packages()? Thanks a gain. ...
written 3 months ago by Gary0
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Package is not available for R version 3.5.0
... Hi, Using qvalue as an exmple (the detail bleow), I cannot install it for R 3.5.0. It is the same for other packages I need. Anyone can help me? Many thanks. > require(NBPSeq) Loading required package: NBPSeq Error: package or namespace load failed for ‘NBPSeq’ in loadNamespace(j <- i[[1L]] ...
qvalue nbpseq written 3 months ago by Gary0 • updated 3 months ago by Gordon Smyth35k
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Comment: C: How to change sample names in featureCounts or edgeR
... Thank you so much! ...
written 4 months 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 4 months ago by Gary0 • updated 4 months ago by Gordon Smyth35k
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Comment: C: How edgeR reads an R List object produced by featureCounts
... Thank you so much. ...
written 4 months 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 4 months ago by Gary0 • updated 4 months ago by Gordon Smyth35k
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Comment: C: Could not find function "makeTranscriptDbFromGFF"
... You are right and thank you so much. ...
written 12 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 12 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 12 months ago by Gary0 • updated 12 months ago by Michael Lawrence10k
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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 13 months ago by Gary0 • updated 13 months ago by Rory Stark2.6k

Latest awards to Gary

Supporter 12 months ago, voted at least 25 times.
Popular Question 21 months ago, created a question with more than 1,000 views. For How to run the rpkm function of edgeR
Popular Question 21 months ago, created a question with more than 1,000 views. For DiffBind installation doesn't work

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