User: aec

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aec50
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Posts by aec

<prev • 71 results • page 1 of 8 • next >
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Comment: C: removing genes before RNA-seq normalization
... Thanks Gordon, then I was wrong. I thought one can not modify the RNA composition of the sample bioinformatically before the normalization. ...
written 5 days ago by aec50
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removing genes before RNA-seq normalization
... Dear all, Removing genes manually before RNA-seq normalization is not a good practice, right? For example, we would like to investigate osteoblast expression from bone samples, but we know that there is some contamination from muscle. Is it correct to remove the 'muscle' genes before normalization? ...
normalization edger deseq2 removing genes written 7 days ago by aec50 • updated 7 days ago by Gordon Smyth39k
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Comment: C: edgeR /DESeq2 normalization for differential expression in RNA-seq blood samples
... The RNA-seq samples have already been sequenced (without globin depletion). ...
written 9 months ago by aec50
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edgeR /DESeq2 normalization for differential expression in RNA-seq blood samples
... Dear all, Both DESeq2 and edgeR normalization methods take into account different library sizes and RNA composition between samples, but are they able to account for a high difference of hemoglobin content in human blood samples? In my experiment, a single globin gene consumes between 2% - 50% of t ...
rnaseq normalization edger deseq2 hemoglobin written 9 months ago by aec50 • updated 9 months ago by Ryan C. Thompson7.4k
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Comment: C: time series, block by patient, between and within comparisons limma-voom
... Thanks Aaron, it worked perfectly. Now if I am interested in applying LRT method to detect differential genes between the two time-courses over time, how to set up the model with limma? 5 time-points is enough for using splines? ...
written 13 months ago by aec50
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Comment: C: time series, block by patient, between and within comparisons limma-voom
... Yes, irrespective of the group. ...
written 14 months ago by aec50
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Comment: C: time series, block by patient, between and within comparisons limma-voom
... I have 5 time points per patient, in total 15 patients. These 15 patients can be further divided in two groups for question b) ...
written 14 months ago by aec50
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Comment: C: time series, block by patient, between and within comparisons limma-voom
... sure, I will edit my post. ...
written 14 months ago by aec50
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time series, block by patient, between and within comparisons limma-voom
... Dear all, I have a time course RNA-seq analysis with the following design: 5 time points, 15 patients, 2 types of patients. the questions I would like to answer: a) expression differences across time points irrespective of patient type (t1 vs t2, t1 vs t3, ...) b) expression differences between ...
rna-seq patient limma-voom time series written 14 months ago by aec50 • updated 14 months ago by Aaron Lun25k
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Comment: C: differential expression analysis with big dataset and >500 surrogate variables
... thanks Michael.  ...
written 18 months ago by aec50

Latest awards to aec

Popular Question 13 months ago, created a question with more than 1,000 views. For order of covariates for GLM with edgeR
Popular Question 13 months ago, created a question with more than 1,000 views. For How to deal with up to 75% of DE genes in RNA-seq (TMM, edgeR) ?
Popular Question 13 months ago, created a question with more than 1,000 views. For normalization affects drastically limma-voom + sva results
Popular Question 14 months ago, created a question with more than 1,000 views. For order of covariates for GLM with edgeR
Popular Question 2.4 years ago, created a question with more than 1,000 views. For limma - complex design with paired samples, sex and batch effect

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