User: e.antoun

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e.antoun20
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Location:
United Kingdom
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2 years, 8 months ago
Joined:
3 years, 7 months ago
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e*******@hotmail.co.uk

Posts by e.antoun

<prev • 11 results • page 1 of 2 • next >
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Comment: A: RNAseq continuous variable outliers
... Sorry for posting this, but does anyone have any ideas on what I can do with this? Thanks ...
written 2.7 years ago by e.antoun20
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Comment: C: RNAseq continuous variable outliers
... I have added it to the original post. Hopefully that'll make things a bit clearer ...
written 2.7 years ago by e.antoun20
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Answer: A: RNAseq continuous variable outliers
... Just to add, I have tried using edgeR, voom+limma and I have the same problem, where there is 1 or 2 samples that seem to be skewing the data and appears to be an outlier, but still coming up and highly differentially changed. Thanks ...
written 2.7 years ago by e.antoun20
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Comment: C: RNAseq continuous variable outliers
... Thanks for the reply. The 'very last sample' just happens to be the last sample in the data frame above, sample 38. Fast is indeed the variable, it is the percentage of fast fibres in a muscle sample. Total, there are 40 samples, the samples are grouped based on disease status, with the first 17 as ...
written 2.8 years ago by e.antoun20
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RNAseq continuous variable outliers
... Hi, I am attempting to analyze some RNAseq data with respect to a couple of continuous variables. I am using DESeq2 in R to do this, but am running into a problem. Below is the code I am using: dds <- DESeqDataSetFromHTSeqCount(samples, directory=".", design=~fast) dds <- DESeq(dds) ...
rnaseq outlier deseq2 continuous written 2.8 years ago by e.antoun20
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Answer: A: Cutadapt installation problem
... Problem solved, I needed to put my locally installed cutadapt version into my PATH, as the older version was installed on the system that I don't have admin access to. ...
written 3.4 years ago by e.antoun20
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Comment: C: Cutadapt installation problem
... Thanks for the reply. The output of which cutadapt is: /local/software/python/2.7.5/bin/cutadapt and echo $PATH gives: /local/software/python/2.7.5/bin/:/usr/lib64/qt-3.3/bin:/local/software/moab/default/sbin:/local/software/moab/default/bin:/local/software/torque/default/sbin:/local/software/torq ...
written 3.4 years ago by e.antoun20
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Cutadapt installation problem
... Hi, I am attempting to install the latest version of cutadapt (1.9) using the source code. I have downloaded cutadapt-1.9.tar.gz, extracted it and ran the following: python setup.py install --user.   Cutadapt install fine, but then when I check the version, it says I have installed version 1.3. ...
cutadapt written 3.4 years ago by e.antoun20
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Comment: C: RNA-seq analysis without grouping data
... Thanks for the reply, I shall have a look at the GLM capabilities of edgeR and DESeq. ...
written 3.6 years ago by e.antoun20
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Comment: C: RNA-seq analysis without grouping data
... Thanks for the reply, that is one possibility but it is what we are hoping to avoid having to do, as it is technically still grouping the data. Obviously if there is no way around it, then we will have to go down that route,, but we are hoping to avoid that as much as possible. ...
written 3.6 years ago by e.antoun20

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