User: ashley.doane

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ashley.doane20
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United States
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1 month ago
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3 years, 3 months ago
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Posts by ashley.doane

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Comment: C: DESEq2 Error in `rownames<-`(`*tmp*`, value = names(x))
... Thanks, this solves the immediate issue.  I dont think it would matter, but failed to mention it was a large counts matrix by number of rows, as there were 103,000 "genes" (ATACseq peaks). Please let me know if I can provide additional information. And also, thanks so much for DESeq2 and for conti ...
written 5 weeks ago by ashley.doane20
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DESEq2 Error in rownames<-(*tmp*, value = names(x))
... Hi, Getting an unexpected error with DESeq2.   > dds = DESeq(dds) using pre-existing normalization factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing -- replacing outliers and refitting for 792 genes - ...
deseq2 software error written 5 weeks ago by ashley.doane20 • updated 4 weeks ago by Michael Love20k
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Epivisr namespace error
... Hi, With an updated Bioconductor, I get the following error loading the epivisr package.  Any suggestions for a possible fix would be great. library(epivizrStandalone) Loading required package: epivizr Error : .onLoad failed in loadNamespace() for 'epivizrStandalone', details: call: file(file, ...
epivizr written 2.5 years ago by ashley.doane20 • updated 2.5 years ago by Hector Corrada Bravo60
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Answer: A: Problem with biomart's listMarts function
... This seems to be not working again.  Please share if you know a solution! > library(biomaRt) > ensembl=useMart("ensembl") > ensembl=useMart("ensembl") ​Space required after the Public Identifier SystemLiteral " or ' expected SYSTEM or PUBLIC, the URI is missing Error: 1: Space required ...
written 2.6 years ago by ashley.doane20
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ChipQC report tables
... Is it possible to generate the html QC tables with a call to ChIPQCreport(), that does not include the commentary and interpretation narrative?   thanks Ashley   ...
chipq written 2.6 years ago by ashley.doane20 • updated 2.5 years ago by Thomas Carroll400
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motifbreakR VariantAnnotation namespace error on reading vcf file
... Hi I'm encountered the following error while reading a vcf file using the motifbreakR package.     vcf <- "/Users/asd2007/Tools/vcftools/examples/annotate-test.vcf" vars <- snps.from.file(file =vcf, search.genome = BSgenome.Hsapiens.UCSC.hg19, format = "vcf") Error: 'seqlevels<-' is ...
variantannotation motifbreakr written 3.0 years ago by ashley.doane20 • updated 3.0 years ago by Simon Coetzee40
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Answer: A: subset of samples from dba object in DiffBind
... Thanks Rory! ...
written 3.1 years ago by ashley.doane20
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subset of samples from dba object in DiffBind
...   Is it possible to create a new dba object based on a subset of the samples in a previous call to dba.count, or dba.analyze?   Basically, I would like analyze subsets of samples as seperate analyses, without recounting.  I'm analyzing atac-seq data, which is paired end and >50 million reads p ...
diffbind written 3.2 years ago by ashley.doane20
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How to annotate DESeq2 object with gene size to get FPKMs
... I'd like to annotate a DESeqDataSet with information on gene size, specifically populating mcols(dds)$basepairs, where dds is my DESeqDataSet.  The DESeqDataSet was created from HTSeq output, using the DESeqDataSetFromHTSeqCount function.           The reason for this is to pull out FPKMs, and ...
deseq2 fpkm written 3.3 years ago by ashley.doane20 • updated 3.3 years ago by Michael Love20k

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Popular Question 17 months ago, created a question with more than 1,000 views. For How to annotate DESeq2 object with gene size to get FPKMs
Popular Question 17 months ago, created a question with more than 1,000 views. For subset of samples from dba object in DiffBind

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