User: gdeniz

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gdeniz0
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Posts by gdeniz

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Comment: C: How to normalize RNA-seq data if majority of transcripts expected to be differen
... I am working with a factor that is part of the general transcription machinery thus I would expect most genes to be downregulated. I see a reduction in the meta gene analysis for all genes from TSS to TTS, but strangely it is not really evident in the MA plots after using edgeR. ...
written 6 weeks ago by gdeniz0
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Comment: C: How to normalize RNA-seq data if majority of transcripts expected to be differen
... Thanks for your reply. ...
written 6 weeks ago by gdeniz0
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How to normalize RNA-seq data if majority of transcripts expected to be differentially expressed vs control condition?
... Hi, I am using edgeR to analyze a knockout cell line vs WT control and expect a major fraction of transcripts differentially expressed. Using default settings with edgeR I could confirm significant downregulation of my knocked out transcript. However, given the following statement in the edgeR manua ...
rnaseq edger written 6 weeks ago by gdeniz0 • updated 6 weeks ago by Gordon Smyth39k
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makeBackground error message "Sequence only contain N's"
...   Hi, when I run the example in the makeBackground help file with the quick option set to "F", I get an error: Error in motifScores(bg, pwms, verbose = verbose) :    Sequence with index(es): 49007,49008,49171,49172,49173,49174 only contain N's. Please remove this sequence as the PWM score cannot ...
pwmenrich written 18 months ago by gdeniz0
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Row clustering featureAlignedHeatmap function (ChipPeakAnno package)
... Hi, is there a way to cluster rows of the heatmaps produced by featureAlignedHeatmap() from the ChipPeakAnno package by signal from left to right? This is a nice way to show co-binding of a second TF at regions centered at binding sites for the first TF. Thanks for your input.  Best, Deniz     ...
chippeakanno heatmap written 18 months ago by gdeniz0 • updated 18 months ago by Ou, Jianhong1.2k

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