User: Matthew Thornton

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280
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USA, Los Angeles, USC
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1 year ago
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Posts by Matthew Thornton

<prev • 25 results • page 1 of 3 • next >
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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 13 months ago by Matthew Thornton280
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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 3.3 years ago by Matthew Thornton280 • updated 3.3 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 3.4 years ago by Matthew Thornton280
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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 3.4 years ago by Matthew Thornton280 • updated 3.4 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 3.4 years ago by Matthew Thornton280 • updated 3.4 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 3.6 years ago by Matthew Thornton280 • updated 3.6 years ago by Martin Morgan ♦♦ 20k
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VSN after xps with RaGene2.0ST chips - is there a way to keep an identifier?
... Hello! I am using the vsn package to process Rat Gene 2.0 ST chips. I have to export the data from xps and put the data into vsn as a matrix. The data going into vsn has column names corresponding to "X" and "Y" locations and the MEAN intensity for each sample. I call vsn with ' fit <- vsn2(as. ...
vsn process xps written 3.7 years ago by Matthew Thornton280 • updated 3.7 years ago by Wolfgang Huber13k
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Is there an expected coefficient of variation for the hybridization probe intensities among technical replicates?
... Hello! I am digging through the control intensities for technical replicates obtained with an Affymetrix GeneChip Rat Gene 2.0 ST array. I have 3 technical replicates of the same sample. The kernel density plot overlay of the raw data shows differences in the intensity distributions. When I pull ...
probe written 3.7 years ago by Matthew Thornton280 • updated 3.7 years ago by cstrato3.8k
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Comment: C: Limma design and contrast matrix question.
... Hi James, Thank you for your reply! > Not really. This is the point at which I start the experimental design grilling session. Why did you do the combination treatment? What did you expect to see (e.g., what is your hypothesis that you are testing)? Yes, we are expecting synergy between the tr ...
written 3.8 years ago by Matthew Thornton280
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Comment: C: Limma design and contrast matrix question.
... Hi Dario! Thank you for your reply. I am glad that I have a proper design matrix. I will try the 'Group1 -Group2 -Group3 + Control' contrasts.matrix. I am not very experienced with general linear models. So let me guess why that would be an appropriate contrast matrix, is it because the null hypoth ...
written 3.8 years ago by Matthew Thornton280

Latest awards to Matthew Thornton

Great Question 12 months ago, created a question with more than 5,000 views. For Limma design and contrast matrix question.
Popular Question 12 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 3.3 years ago, created a question with more than 1,000 views. For Limma design and contrast matrix question.

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