User: Emmanouela Repapi

Reputation:
20
Status:
New User
Location:
United Kingdom
Last seen:
2 months, 1 week ago
Joined:
5 years, 7 months ago
Email:
e****************@imm.ox.ac.uk

Posts by Emmanouela Repapi

<prev • 9 results • page 1 of 1 • next >
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Comment: C: nested modeling for unequal groups with edgeR
... Thank you for your answer Ryan! In my mind the cell factor is also nested within the sort because the positive cells are specific for the sort in question. There shouldn't be a great difference in the negative cells of the two sorts because they are just the remaining cells from either sort. Althoug ...
written 3.5 years ago by Emmanouela Repapi20
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nested modeling for unequal groups with edgeR
... Hello,  I have a fairly complicated design of experiment and I would like some help/feedback on designing the model.matrix. The data is coming from an experiment for which there are two groups of mice (young/old), the cells of which have been used for sorting populations with two markers (sort1/sor ...
edger r edger de written 3.5 years ago by Emmanouela Repapi20 • updated 3.5 years ago by Ryan C. Thompson7.4k
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Comment: C: negative values for trended dispersion with edgeR
... That worked! Thank you Yunshun! ...
written 4.2 years ago by Emmanouela Repapi20
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negative values for trended dispersion with edgeR
... Hello,  I have a dataset with very high coverage on each sample for which I want to run edgeR on to get the differentially expressed transcripts between 2 types of cells with 3 replicates each.  The analysis runs smoothly and I have many DE transcripts, but when I plot the BCV I get a plot (which i ...
rnaseq edger estimatedispersions written 4.2 years ago by Emmanouela Repapi20 • updated 4.2 years ago by Yunshun Chen540
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Comment: C: Error for plotDEXSeq and warning for estimateDispersions
... That's what I thought too. Thanks for clarifying.  Emmanouela ...
written 5.2 years ago by Emmanouela Repapi20
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Comment: C: Error for plotDEXSeq and warning for estimateDispersions
... Hi Alejandro, Here is the code that I used to get the counts objects: module load HTSeq python /Filers/package/R/3.0.1/lib64/R/library/DEXSeq/python_scripts/dexseq_prepare_annotation.py ensembl_hg19_genes.gtf ensembl_hg19_genes_flattened.gtf python /Filers/package/R/3.0.1/lib64/R/library/DEXSeq/py ...
written 5.2 years ago by Emmanouela Repapi20
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Error for plotDEXSeq and warning for estimateDispersions
... Hello, I have been trying to use DEXSeq to do a DEU analysis and plot some of the genes that are coming up in the results. The analysis seems to be working fine (even though I am getting a warning when I estimate the dispersion) and I have about 2000 hits, but when I try to visualise the difference ...
graph dexseq written 5.2 years ago by Emmanouela Repapi20 • updated 5.2 years ago by Alejandro Reyes1.7k
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Comment: C: use of voom function with attract package
... Dear Gordon, Ok, that’s what I thought. Thank you again so much for all your help! Best wishes, Emmanouela Emmanouela Repapi, PhD Computational Biology Research Group Weatherall Institute of Molecular Medicine University of Oxford, OX3 9DS Tel: (01865 2)22253 On 25 Apr 2014, at 00:25, Gordon K ...
written 5.6 years ago by Emmanouela Repapi20
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Comment: C: use of voom function with attract package
... Dear Gordon and Ryan, Thank you both very much for your replies, using the F statistic from the lmFit and the geneSetTest seems like the right way to go for what I need to do. On a similar note, do you have a function in mind for finding the genes with similar expression profiles within a specific ...
written 5.6 years ago by Emmanouela Repapi20

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Popular Question 3.5 years ago, created a question with more than 1,000 views. For Error for plotDEXSeq and warning for estimateDispersions

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