User: Colari19

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Colari1940
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Posts by Colari19

<prev • 10 results • page 1 of 1 • next >
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Is it possible to run Matrix eQTL with multiple samples per patient?
... I have RNA-Seq data and SNP data for 60 patients before (baseline) and one week after a drug treatment. I'd like to use Matrix eQTL to identify eQTLs in these patients and see if there is a difference in the effect size of these eQTLs before and after treatment. My first instinct was to run Matr ...
R eqtl rna-seq written 22 days ago by Colari1940
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How to compare two sets of results from Limma?
... Hi, Say I've carried out two differential expression analyses using the limma-voom pipeline on two datasets, A and B. How could one go about comparing the results from these two analyses to see how similar or different they are? For example, there may be genes that are differentially expressed in ...
R limma rna-seq voom written 7 weeks ago by Colari1940 • updated 6 weeks ago by kristoffer.vittingseerup3.0k
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Comment: C: Visualisation of SNPs in R
... Thank you, this is exactly the kind of thing I'm after. ...
written 11 weeks ago by Colari1940
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Visualisation of SNPs in R
... Does anyone have any suggestions of how best to visualise SNP locations in relation to their nearest gene? Is there a standard way of doing this? Any good bioconductor packages available? I have a list of cis-eQTL SNPs along with their target genes (eGenes). I'd like to draw the location of the eQT ...
gene R snp written 11 weeks ago by Colari1940
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Comment: C: Functional analysis of RNASeq differentially expressed genes
... Thank you for your very informative response. ...
written 3 months ago by Colari1940
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Functional analysis of RNASeq differentially expressed genes
... Hi, I have a few questions about how best to derive more intuitive biological meaning from a differential expression analysis of RNASeq data. So far I have been using two approaches: (1) Perform differential expression analysis with Limma, then input DEGs that meet a given significance threshold ...
camera rna-seq ipa gsea limma written 3 months ago by Colari1940 • updated 3 months ago by h.mon29k
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Defining the design for a complicated multi-level experiment in Limma
... Hello, I've carried out a number of differential expression analyses using the Limma-Voom pipeline for a rather complicated data set. I'd just like to clarify that my approach detailed below is appropriate. The design of the experiment is very much like those described in sections 9.6 and 9.7 of t ...
R limma rna-seq voom written 4 months ago by Colari1940
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Comment: C: Voom with QuSAGE
... Thank you for your answer! I'll try CAMERA instead. ...
written 4 months ago by Colari1940
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Voom with QuSAGE
... Hi, Does anyone know if voom-normalised counts are compatible with QuSAGE, or should I just use the edgeR cpm function to get log2 expression counts? I'd rather use voom for consistency across my different analyses, but I'm not sure if the precision weights pose a problem for QuSAGE... Thank you. ...
R qusage limma rna-seq voom written 4 months ago by Colari1940 • updated 4 months ago by Gordon Smyth1.4k
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How to merge Kallisto TSV files for use with Tximport
... I have pseudo-aligned some RNASeq reads using Kallisto where each sample was split over two flow cells. I pseudo-aligned the fastq files for each flow cell separately, meaning for each sample I have two abundance TSV files that look like this: target_id length eff_length est_counts tpm ...
tximport R kallisto rna-seq written 8 months ago by Colari1940

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