User: aec

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aec30
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Posts by aec

<prev • 37 results • page 1 of 4 • next >
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how to extract complex contrast with DESeq2
... Hi, I have the following RNA-seq experiment: control (right tissue) vs control (left tissue) case (right tissue) vs case (left tissue) I would like to find the DE genes present in the first comparison + DE genes second comparison but discarding those DE genes that are significant in both compari ...
deseq2 contrast differential gene expression written 14 days ago by aec30 • updated 13 days ago by Michael Love12k
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differential expression with heterogenous disease
... Dear all, How to deal with a very heterogenous dataset for DE analysis? i.e, each of the affected individuals respond differently to treatment or heterogenous disease which is hard to detect any common DE gene wit hrespect to controls? Is there a way to obtain each patient difference individually ...
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Comment: C: How to deal with up to 75% of DE genes in RNA-seq (TMM, edgeR) ?
... Aaron, the logratioTrim is a parameter of edgeR I can change ? The option of adding spike-ins is not duable right now, would it be a proper approximation of trusting only DE genes with extreme fold change i .e FC >2 or FC>4 ? ...
written 6 weeks ago by aec30
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Comment: C: How to proceed with different degradation levels of RNA-seq samples?
... Thanks Aaron. In my case PC1 is separating the outliers from the rest (50% variance), what is better to correct for PC1 in my model design or just add a covariate with high/low quality as you pointed? Other option would be trying this methodology: http://biorxiv.org/content/early/2016/09/09/07424 ...
written 6 weeks ago by aec30
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How to deal with up to 75% of DE genes in RNA-seq (TMM, edgeR) ?
... Dear all, The drug effects are so drastic that the cell lines have more than 75% of the genes differentially expressed (3 control vs 3 treatment). I used the TMM normalization and EdgeR for the analysis, which assume a maximum of 60% of differentially expressed genes. How to proceed with such a cas ...
rnaseq normalization edger differential expression tmm written 6 weeks ago by aec30
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How to proceed with different degradation levels of RNA-seq samples?
... Dear all, I am dealing with a mixture of high/low complexity RNA-seq libraries, some of RNA samples had low RIN values (~4) and others high (>8) all coming from human brain tissue. I found high proportion of multimapping reads (~40%) for the most affected and a different proportion of gene bioty ...
brain differential expression rna-seq degradation variability written 6 weeks ago by aec30 • updated 6 weeks ago by Aaron Lun14k
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Comment: C: How different ploidy affect differential expression analysis with RNA-seq
... very interesting, thanks for the reflection Aaron. ...
written 6 weeks ago by aec30
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How different ploidy affect differential expression analysis with RNA-seq
... Dear all, I have two related questions: 1) Are the assumptions for normalization violated when comparing experimental conditions with different ploidy? 2) Does it make sense to perform differential expression analysis between them with RNA-seq? Expression is going to be confounded with the number ...
normalization differential expression rna-seq ploidy assumption written 6 weeks ago by aec30 • updated 6 weeks ago by Aaron Lun14k
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Comment: C: edgeR time series DMSO correction
... ok, thanks. ...
written 6 months ago by aec30
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Comment: C: edgeR time series DMSO correction
... So apart from testing independently these two contrats: 4h.treat - 4h.control 4h.control - 0h There is no other way to test the treatment effect (respect to time 0h) corrected by any effect of the DMSO (respect to time 0h)  at the same time?  ...
written 6 months ago by aec30

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