User: guillaume.rbt

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guillaume.rbt620
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Posts by guillaume.rbt

<prev • 170 results • page 1 of 17 • next >
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Comment: C: RNA-seq differential expression : relevance of mixing several datasets
... The experimental designs are quite consistent on the paper, but as it is tumor biopsies samples, I'm afraid the different procedures associated with samples treatment can bring a lot of noise. ...
written 6 days ago by guillaume.rbt620
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RNA-seq differential expression : relevance of mixing several datasets
... Hi all, I'm currently doing differential expression analysis on several public RNAseq datasets coming from different studies. Each one having samples with two conditions : "responders" and "non responders". I'm wondering if I should analyse each dataset separately or if I should mix all samples i ...
rna-seq differential expression written 6 days ago by guillaume.rbt620 • updated 6 days ago by leaodel80
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Comment: C: RNA-seq differential expression analysis with high number of samples
... Ok I get it! Out of curiosity, if there is no intersection in the results of all datasets analysed independently, is there any chance that I would find differentially expressed genes by merging all datasets and analyzing it as a whole? ...
written 12 days ago by guillaume.rbt620
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Comment: C: RNA-seq differential expression analysis with high number of samples
... Ok I will try this way! Thanks ...
written 14 days ago by guillaume.rbt620
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Comment: C: RNA-seq differential expression analysis with high number of samples
... For now I combined 3 studies, I've dealt with batch effect with the DEseq2 design (design = ~study + response), but I don't know to which extent it would correct the biases. What do you mean by meta-analysis? Should I use specifics tools designed for meta-analysis? ...
written 14 days ago by guillaume.rbt620
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Comment: C: RNA-seq differential expression analysis with high number of samples
... Thank for your feedback. I indeed have batch effect, that I've tried to correct within my Deseq2 design (design = ~study + response). When you mention data-wise analysis, do you mean that I should analyse each dataset separatly, and then cross the different results? ...
written 14 days ago by guillaume.rbt620
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RNA-seq differential expression analysis with high number of samples
... Hi all, I'm currently doing a differential expression analysis on a high number of samples (>100), mixing samples from different public datasets. I've used Deseq2 so far, but I'm getting strange results, where some genes are given significantly differentially expressed, but with very high expre ...
rna-seq differential expression written 14 days ago by guillaume.rbt620 • updated 13 days ago by Charles Warden7.0k
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Answer: A: Identifying unique SNPs between species
... I've dealed with the same type of analysis. My solution was to do a pooled genotyping thanks to the GATK "best practices" pipeline, to obtain a single multi-sample VCF with the called genotypes of all my samples. Then I filtered this VCF to obtain SNPs unique to each sample, for that you can use " ...
written 4 weeks ago by guillaume.rbt620
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Answer: A: RNA Seq analysis of rice samples
... I'm not a specialist of the rice genome but it seems that it has a lot of duplicated genes. See here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC546038/ ,where it says "We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome" This might explain the high number of multi- ...
written 4 weeks ago by guillaume.rbt620
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Comment: C: Relevance of RNAseq meta-analysis
... Ok thanks, I will keep in mind those constraints. ...
written 4 weeks ago by guillaume.rbt620

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Popular Question 3 months ago, created a question with more than 1,000 views. For Comparing gff files
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