User: Ar

gravatar for Ar
Ar650
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650
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United States
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aayushraman
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3 weeks, 3 days ago
Joined:
1 year, 9 months ago
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Posts by Ar

<prev • 77 results • page 1 of 8 • next >
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Comment: C: ComBat (SVA) Application - Two Technical Effects
... I am sorry but for some reason the post came up on the "Biostars Latest question". I think it was because the Biostar modified your post. However, thanks for sending the paper. I will go through it. ...
written 4 months ago by Ar650
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Comment: C: ComBat (SVA) Application - Two Technical Effects
... Here is my earlier post on Batch Correction: https://www.biostars.org/p/196430/#196528 I would recommend you to combine all the dataset you have and then get the batch information using sva function. Now sva gives you surrogate variables (which is batch plus information about other latent variables ...
written 4 months ago by Ar650
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DESeq2 design and interaction terms
... I went through the vignette about interaction terms and would like to understand if I am applying interaction terms correctly and biologically, if I am extracting the correct the terms. Here is the example code from DESeq2 R documentation for **two conditions (A, B) and three genotypes (I,II,III)**. ...
R deseq2 rna-seq written 5 months ago by Ar650
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Answer: A: PCA tpm fpkm
... I would recommend to do log-transformation of the TPM/RSEM dataset. PCA has a hidden assumption of normality. PCA finds the coordinate system such that it can maximize the variance between the points. This achieved using orthogonal principal components. In case of multivariate Gaussian distribution ...
written 5 months ago by Ar650
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Comment: C: Difference between the Fasta files from UCSC and Gencode/Ensembl
... Thanks and that was an awesome answer! Actually you made my stupid question look good! :D ...
written 5 months ago by Ar650
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Comment: C: Difference between the Fasta files from UCSC and Gencode/Ensembl
... Thanks a lot. That was helpful! ...
written 5 months ago by Ar650
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Comment: C: Recommended cutoff for FDR - 0.05 or 0.1
... WouterDeCoster: Mostly in small sample size where n = 4 or 5 for each genotype (in a model organism such as mice). ...
written 5 months ago by Ar650
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Comment: C: Recommended cutoff for FDR - 0.05 or 0.1
... In most of the brain tissues like Hypothalamus, cerebellum, straitum and dentate gyrus. Typically, people use anova rather then limma. Limma gives you around 20-30 genes where as anova gives you 100-200 genes. The transcriptomic changes are very small and most of diff expressed genes between WT and ...
written 5 months ago by Ar650
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Comment: C: Recommended cutoff for FDR - 0.05 or 0.1
... I totally agree with Daniel's first paragraph but not second. There are many mendelian diseases (like Rett Syndrome) where the phenotype is extremely different however, the number of diff expressed genes between a WT and KO model organism is very small (~20 to 30 max with FDR < 0.05). Then I thin ...
written 5 months ago by Ar650
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Answer: A: Recommended cutoff for FDR - 0.05 or 0.1
... You may use FDR or 0.1 if the number of diff. expressed genes (DEGs) from DESeq2 is not large (>100 or more). Typically FDR of 0.1 means that there is a chance that 10% of the genes are not false positive i.e. if 100 genes are called DEGs then about 10 genes are false positive. However, if the n ...
written 5 months ago by Ar650

Latest awards to Ar

Good Answer 9 weeks ago, created an answer that was upvoted at least 5 times. For A: Beginner in Bioinformatics / computational biology field
Student 9 weeks ago, asked a question with at least 3 up-votes. For Difference between the Fasta files from UCSC and Gencode/Ensembl
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Public paired end chip seq dataset, both ChIP and input?
Supporter 7 months ago, voted at least 25 times.
Appreciated 8 months ago, created a post with more than 5 votes. For A: Limma strange low p-values.
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Beginner in Bioinformatics / computational biology field
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Public paired end chip seq dataset, both ChIP and input?
Scholar 8 months ago, created an answer that has been accepted. For A: Public paired end chip seq dataset, both ChIP and input?
Scholar 8 months ago, created an answer that has been accepted. For A: Public paired end chip seq dataset, both ChIP and input?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Public paired end chip seq dataset, both ChIP and input?
Scholar 8 months ago, created an answer that has been accepted. For A: Public paired end chip seq dataset, both ChIP and input?
Scholar 8 months ago, created an answer that has been accepted. For A: Public paired end chip seq dataset, both ChIP and input?
Appreciated 8 months ago, created a post with more than 5 votes. For A: Limma strange low p-values.
Scholar 8 months ago, created an answer that has been accepted. For A: Public paired end chip seq dataset, both ChIP and input?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Public paired end chip seq dataset, both ChIP and input?
Scholar 8 months ago, created an answer that has been accepted. For A: Public paired end chip seq dataset, both ChIP and input?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Public paired end chip seq dataset, both ChIP and input?

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