User: Gary

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Gary0
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Posts by Gary

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Comment: C: Could not find function "makeTranscriptDbFromGFF"
... You are right and thank you so much. ...
written 8 weeks 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 weeks 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 8 weeks ago by Gary0 • updated 8 weeks ago by Michael Lawrence9.8k
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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 weeks ago by Gary0 • updated 9 weeks ago by Rory Stark2.1k
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Comment: C: How DiffBind run PCA based on peak data?
... I really appreciate your detailed and clear explanation. Gary ...
written 10 weeks 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 10 weeks ago by Gary0
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How DiffBind run PCA based on peak data?
... May I know how DiffBind analyze peak present/absent data for a PCA analysis? The traditional PCA needs continuous values with the normal distribution. Does DiffBind use a non-parametric method? Or DiffBind use scores (e.g. FDR value) for each peak to perform PCA? Many thanks. ...
diffbind written 10 weeks ago by Gary0 • updated 10 weeks ago by Rory Stark2.1k
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Comment: C: There is no dba.plotVolcano function in DiffBind and how to upgrade DiffBind to
... Thanks a lot ...
written 10 weeks ago by Gary0
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Can ChIPQC analyze mandarin duck ChIP-Seq data?
... Hi, I am analyzing mandarin duck (Aix galericulata) ChIP-Seq data. We have a mandarin duck genome assembly .fa file and a genome annotation .gff file produced by our cooperators. May I know whether ChIPQC can analyze mandarin duck histone modification ChIP-Seq data? Could you show me how to do it, ...
chipqc written 10 weeks ago by Gary0 • updated 8 weeks ago by Thomas Carroll390
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Comment: C: There is no dba.plotVolcano function in DiffBind and how to upgrade DiffBind to
... I have installed R 3.4. However, when I run dba.report() with bDB = TRUE, and bNotDB = TRUE, I can see the corresponding values in Global Environment, but there is still no the corresponding file in my working directory (the detail below). Could you help me more? Many thanks. h3k27ac.DB <- dba.r ...
written 11 weeks ago by Gary0

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