User: Matthew Thornton

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USA, Los Angeles, USC
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Posts by Matthew Thornton

<prev • 29 results • page 1 of 3 • next >
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Comment: C: DEXSeqHTML and biomart object
... Ok so this looks like the answer to my question, sorry I didn't see it first.  I am confused, how do you know for sure that the 'ensembl_gene_id' lines up with the 'ensembl_gene_id' in dxr?  I guess because you pull from it  initially with values=geneIDs(dxd)?  Thanks!! ...
written 8 weeks ago by Matthew Thornton290
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Comment: C: Annotation of DEXSeqHTML with biomaRt
... Could you post as an answer how you would add annotations using DEXSeqHTML?  I would be nice to have more, info, like the descriptions, but I would settle for just the external_gene_names. Could it be that there is not enough room in HTML table? ...
written 8 weeks ago by Matthew Thornton290
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Comment: C: Annotation of DEXSeqHTML with biomaRt
... I will try this. Can a vector be used with the attributes switch with DEXSeqHTML? Thank you! ...
written 8 weeks ago by Matthew Thornton290
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Annotation of DEXSeqHTML with biomaRt
... Hello!  I am trying to annotate the output of DEXSeqHTML for ease of my collaborators.  I am using the code but not getting any annotation. Does anyone else have this problem? DEXSeqHTML(dxr1, genes=NULL, path="DEXSeqReport", file="testForDEU.html", fitExpToVar="condition", FDR=0.1, color=NULL, co ...
biomart dexseq written 9 weeks ago by Matthew Thornton290
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Figuring out what long decent Phred value unaligned reads are
... Hello! My question is about reads that don't align to the genome yet are long and have very good Phred scores. Currently, my workflow is FastQC > Cutadapt > Trimmomatic > RNA-STAR > HTSeq-count > edgeR (RUVSeq) I use gencode genomes with Ensembl IDs and even with the cleanest isolati ...
rnaseq alignment written 19 months ago by Matthew Thornton290
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xps - error in normalize - "Error: Length of non-varying units is zero."
... Hello! I am trying to optimize my data processing with xps. I am getting an error when using the normalize function. It could be due to improper switches. here is the error: > data_norm <- normalize(data_bkgrd, "Normalize_Step2", filedir=outdir, tmpdir="", update = FALSE, select = "pmonly", ...
normalization process xps written 3.9 years ago by Matthew Thornton290 • updated 3.9 years ago by cstrato3.8k
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Comment: C: External RNA controls on Rat Gene ST 2.0 chip lfc ~ 1 after xps rma??
... Thank you for the suggestions! I will look at where the ERCC controls fall in the data. I am thinking to use a paired-down set of the ERCC controls in the 'linear' range and which are within my experimental data. I am planning to use the spike-in probes procedure in the vsn package. I will also try ...
written 4.0 years ago by Matthew Thornton290
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External RNA controls on Rat Gene ST 2.0 chip lfc ~ 1 after xps rma??
... Hello! I am processing Affymetrix gene chip Rat Gene 2.0 ST chips with bioconductor package xps using rma normalization. I have included the ExFold ERCC external RNA controls with 2 mixes of different concentrations. I am able to pull out intensities for the ERCC controls at different points along ...
normalization xps written 4.0 years ago by Matthew Thornton290 • updated 4.0 years ago by Davis, Wade340
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VSN with spike-in probes question
... Hello! I am trying to optimize my data processing based on the addition of ExFold ERCC controls. Ideally I would like to normalize with VSN using the procedure in chapter 7 of the vsn vignette. If I pull out the unprocessed intensities for the ERCC controls, order them by increasing concentration, ...
vsn written 4.0 years ago by Matthew Thornton290 • updated 4.0 years ago by Wolfgang Huber13k
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What is the easiest way to make the GC content and length matrix for package cqn?
... Hello! I have some RNASeq data that I am analyzing with edgeR and I would like to use the cqn package to correct for GC bias. I have aligned the data to the UCSC hg38 genome. >From googling I have found the the bedtools 'nuc' command will give me the GC content with ranges and the length. Prov ...
rnaseq edger cqn written 4.2 years ago by Matthew Thornton290 • updated 4.2 years ago by Martin Morgan ♦♦ 21k

Latest awards to Matthew Thornton

Popular Question 19 months ago, created a question with more than 1,000 views. For Importing RMA processed data into limma for eBayes
Great Question 19 months ago, created a question with more than 5,000 views. For Limma design and contrast matrix question.
Popular Question 19 months ago, created a question with more than 1,000 views. For What is the easiest way to make the GC content and length matrix for package cqn?
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Limma design and contrast matrix question.

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