User: Gary

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Gary0
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Posts by Gary

<prev • 44 results • page 1 of 5 • next >
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How to color different column bars independently using dba.plotHeatmap (DiffBind)?
... Hi, I would like to color (1) the column bar of the antibody factor using "orange", "orchid1", and "mediumpurple1", (2) the column bar of the sex factor using "magenta", and "cyan". The commands I used and the figure I produced are below. Could you teach me how to perform it correctly? In addition, ...
diffbind dba.plotheatmap written 6 weeks ago by Gary0 • updated 5 weeks ago by Rory Stark2.6k
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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 5 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 5 months ago by Gary0 • updated 5 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 5 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 5 months ago by Gary0 • updated 5 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 6 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 6 months ago by Gary0 • updated 6 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 14 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 14 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 14 months ago by Gary0 • updated 14 months ago by Michael Lawrence10k

Latest awards to Gary

Popular Question 5 months ago, created a question with more than 1,000 views. For Could not find function "makeTranscriptDbFromGFF"
Popular Question 5 months ago, created a question with more than 1,000 views. For DiffBind installation doesn't work
Supporter 14 months ago, voted at least 25 times.
Popular Question 23 months ago, created a question with more than 1,000 views. For How to run the rpkm function of edgeR
Popular Question 23 months ago, created a question with more than 1,000 views. For DiffBind installation doesn't work

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