User: dsperley

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dsperley0
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Posts by dsperley

<prev • 15 results • page 1 of 2 • next >
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Comment: C: edgeR: Unusual BCV plot
... Fixed the links. ...
written 4 months ago by dsperley0
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edgeR: Unusual BCV plot
... Hi,  I'm doing an RNA-Seq analysis of blood samples from 28 lyme infected patients  and 13 control samples. The reads were aligned with TopHat2 and read were summarized using featureCounts. When estimating the dispersion, I get a value of 3.29, and the following BCV plot: This looks like somethi ...
edger written 4 months ago by dsperley0 • updated 4 months ago by Gordon Smyth30k
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Error reading GEO files using minfi's readGEORawFile function
... I'm trying to use minfi's readGEORawFile function to read in methylation data from the GEO  series GSE59091, but I keep getting the following error: file<-"GSE59091_unmethylated_methylated_cor.txt" GEO<-readGEORawFile(file,sep=" ",Uname="Unmethylated.signal", + Mname="Methylated.signal") Rea ...
minfi written 7 months ago by dsperley0
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Duplicate Correlation with technical replicates
... I'm using Limma to analyze Illumina 450k methylation data. I'm comparing the methylation (M-Values) in Obese vs Lean subjects, and I have a total of 49 arrays, representing 3 Lean subjects and 11 Obese subjects. Each subject is represented by 3-5 arrays,with the exception of one Lean subject that is ...
limma duplicatecorrelation written 7 months ago by dsperley0 • updated 7 months ago by Ryan C. Thompson5.6k
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Interaction at any time.
... I have set up my model matrix following the example 3.3.4 “interaction at any time”  in the edgeR user guide. My experimental design has 2 strains: KO and WT, and 3 time points, 0h, 12h, and 36h. I’m interested in genes that respond differently to infection between the KO and WT at 12h or 36h.  When ...
edger written 21 months ago by dsperley0 • updated 21 months ago by Aaron Lun14k
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Comment: C: Time course RNA-Seq using edgeR
... Thank-you for your advice on this dataset, I plan to use robust empirical Bayes with glmFit() and glmLRT() ...
written 2.1 years ago by dsperley0
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Comment: C: Time course RNA-Seq using edgeR
... I have looked at the pairwise MA/smear plots, and I see no trend in the plot between the WT samples, or other pairs of samples. So I'm planning to take Gordon's advice, and using robust empirical Bayes. Although, for future reference/curiosity, how would one normalize for a trend in LogFC at higher ...
written 2.1 years ago by dsperley0
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Comment: C: Time course RNA-Seq using edgeR
... I have taken your advice and asked the experimenter if there was anything different about the WT.0h.a, KO.0h, and K0.12h samples;  however, the experimenter has no additional information about the sex or collection of the samples. I have run d <- estimateDisp(RNA_data_filtered, design, robust=T ...
written 2.1 years ago by dsperley0 • updated 2.1 years ago by Gordon Smyth30k
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Comment: C: Time course RNA-Seq using edgeR
... Thanks for noticing, you're right that this was a copy/paste error in the comment - I intended to keep genes with a minimum expression in only one sample- since some treatment groups consist of only one sample. ...
written 2.1 years ago by dsperley0
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Time course RNA-Seq using edgeR
... Hi, I’m analyzing some RNA-Seq data for another investigator.  The experimental design is an infection time course with 10 samples (2 biological replicates for each timepoint except 2), 3 timepoints (0h, 12h, 36h) and two strains of mice (WT, and ATG knockout (KO)): WT.0h.a WT.0h.b WT.12h.a W ...
edger written 2.1 years ago by dsperley0 • updated 2.1 years ago by Gordon Smyth30k

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Popular Question 12 months ago, created a question with more than 1,000 views. For P Value of 0?
Popular Question 12 months ago, created a question with more than 1,000 views. For Time course RNA-Seq using edgeR

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