User: Ron

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Ron680
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680
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Posts by Ron

<prev • 299 results • page 1 of 30 • next >
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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 7 hours ago by Ron680
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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 1 day ago by Ron680
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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 2 days ago by Ron680 • updated 1 day ago by abbey0
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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 11 days ago by Ron680
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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 23 days ago by Ron680
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Comment: C: Pairwise comparisons in Differential Expression
... Rep1 is an annotation I added to make sure that Sample1_day0 and Sample1_day3 are replicates since they need to be paired, while doing pairwise comparison. ...
written 24 days ago by Ron680
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Pairwise comparisons in Differential Expression
... Hi all, I have 4 RNAseq samples, both at Day 0 and Day 3. So total 8 samples. I want to do differential Expression analysis between Day 0 and Day 3,but pairwise. I wanted to confirm if this is The best way to do this is using multi-factor design ? from DEseq2 package. The condition of interest s ...
deseq rna-seq written 24 days ago by Ron680
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Comment: C: Time course experiment in RNASeq
... The pattern means if you have for e.g. 3 classes. A gene can go up in first,up in second class and down in the 3rd class.This is one pattern. Also it could go up in first,up in second and up in third.this is another pattern. Similarly you can have all kinds of combinations and see which pattern is ...
written 5 weeks ago by Ron680
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Comment: C: Time course experiment in RNASeq
... You can try using http://bioconductor.org/packages/release/bioc/html/EBSeq.html EBseq package - will generate all the possible patterns between various conditions,and gives you the results in terms of genes following that pattern. ...
written 6 weeks ago by Ron680
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Comment: C: RNAseq on viral positive samples
... Thanks.I looked at the EBV portal. I am looking for tumor samples , not EBV infected cell lines. FASTQ data for human tumor samples is what I am using for my analysis. ...
written 6 weeks ago by Ron680

Latest awards to Ron

Scholar 28 days ago, created an answer that has been accepted. For A: How to import huge .csv files in R studio?
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: pca analysis for differential gene expression data of microarray samples of simi
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Working with human database in Kraken
Popular Question 3 months ago, created a question with more than 1,000 views. For Database of Ligand and receptor genes
Popular Question 4 months ago, created a question with more than 1,000 views. For Database of Ligand and receptor genes
Popular Question 5 months ago, created a question with more than 1,000 views. For Database of Ligand and receptor genes
Student 6 months ago, asked a question with at least 3 up-votes. For GSEA Preranked analysis on RNA-SEQ
Popular Question 6 months ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: pca analysis for differential gene expression data of microarray samples of simi
Popular Question 8 months ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
Great Question 9 months ago, created a question with more than 5,000 views. For GSEA Preranked analysis on RNA-SEQ
Popular Question 9 months ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
Popular Question 9 months ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
Popular Question 10 months ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
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Popular Question 14 months ago, created a question with more than 1,000 views. For Rank Genes By FPKM for only One Sample
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: pca analysis for differential gene expression data of microarray samples of simi
Popular Question 15 months ago, created a question with more than 1,000 views. For Rank Genes By FPKM for only One Sample
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Popular Question 21 months ago, created a question with more than 1,000 views. For GSEA for RNASEQ
Popular Question 21 months ago, created a question with more than 1,000 views. For Extracting reads from multiple regions

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