User: Ron

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Ron760
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Posts by Ron

<prev • 304 results • page 1 of 31 • next >
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Comment: C: Validating driver genes
... What data did you use for finding driver genes? What detection tool you have used?Can you elaborate on this? ...
written 10 weeks ago by Ron760
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Ratio of samples to do differential expression
... Hi all, I have been doing differential expression for a while.One question that always comes to my mind is regarding the ratio of samples that can be compared between control vs treatment. For e.g. Ideal scenario is to have equal number of controls and treatments. But sometimes when its not possib ...
next-gen rna-seq written 11 weeks ago by Ron760
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Comment: C: Using Cufflinks for Novel Transcripts
... Hi Seidel, Thanks for your response.I thought about creating a novel Transcript ID and use the necessary exons of interest.But I was not sure since this gene above has FPKM of 0.63 as well as all the exons. So if I just take a few of those exons for novel transcript ,wouldnt the expression be same ...
written 3 months ago by Ron760
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Comment: C: Does Cufflinks report chimeric transcripts/fusion genes?
... You can use STAR-fusion or other fusion softwares for finding fusion genes. ...
written 4 months ago by Ron760
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Using Cufflinks for Novel Transcripts
... Hi all, I am working on transcript level expression from RNAseq using cufflinks after STAR alignment. I am primarily interested in a gene which has a wild type transcript and a novel transcript.The wild type transcript has the coordinateds and is known so it is present in the gencode annotation fil ...
cufflinks rna-seq written 4 months ago by Ron760 • updated 4 months ago by seidel6.5k
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Comment: C: Interpreting GSEA results
... Yes , I also think the same . that in their experiment the genes are downregulated when RB1 and RB2 are knocked out, but in our data those genes are up regulated. So can we say that still our data is **related** to those **two genes** being **knocked out / down** ,despite of the fact that the genes ...
written 6 months ago by Ron760
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Comment: C: Interpreting GSEA results
... The data is normalized by DESEQ package while doing differential expression.Thanks for your comment ,however thats not what I asked. I just want to know if my results from differential expression analysis - how they relate with this specific pathway based on the enrichment plot ? ...
written 6 months ago by Ron760
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Interpreting GSEA results
... Hi all, I am working with GSEA results using GSEA pre ranked. My input is list of genes with their log2foldchange as the metric . The genes with log2foldchange were calculated using Differential expression. Now in my GSEA results. I see this pathway plot. The pathway name is RB_P130_DN.V1_DN and ...
next-gen rna-seq gsea written 6 months ago by Ron760 • updated 5 weeks ago by pshubhamoy20
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Comment: C: RNASeq data RPKM
... Yes adding 1 to FPKMS is a good way to take care of this. The fold change of B/A is fine but you have to take log of the fold change. ...
written 6 months ago by Ron760
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Comment: C: Pairwise comparisons in Differential Expression
... I was looking at this post's answer and think this is what I want too: https://www.biostars.org/p/256910/ ...
written 7 months ago by Ron760

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