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User: Ar

gravatar for Ar
Ar • 740
Reputation:
740
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United States
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https://www.linkedin.c...
Twitter:
aayushraman
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6 days, 9 hours ago
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Posts by Ar

<prev • 78 results • page 1 of 8 • next >
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Tool: DASC -- detecting hidden batch effects in gene expression datasets (Array/RNA-Seq/scRNA-Seq)
... **Update**: Our manuscript has been published in Bioinformatics -- https://doi.org/10.1093/bioinformatics/btx635. **Abstract**: We propose a data-adaptive, non-parametric, and non-regression approach to remove the biological signal to prepare the data for batch detection and then apply a semi-NMF ...
scrna-seq R batcheffects tool rna-seq written 11 months ago by Ar • 740
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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 20 months ago by Ar • 740
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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 20 months ago by Ar • 740
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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 20 months ago by Ar • 740
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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 20 months ago by Ar • 740
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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 21 months ago by Ar • 740
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Comment: C: Difference between the Fasta files from UCSC and Gencode/Ensembl
... Thanks a lot. That was helpful! ...
written 21 months ago by Ar • 740
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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 21 months ago by Ar • 740
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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 21 months ago by Ar • 740
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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 21 months ago by Ar • 740

Latest awards to Ar

Popular Question 10 weeks ago, created a question with more than 1,000 views. For List of genes expressed in Brain and different tissues
Scholar 10 weeks ago, created an answer that has been accepted. For A: Public paired end chip seq dataset, both ChIP and input?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Public paired end chip seq dataset, both ChIP and input?
Popular Question 4 months ago, created a question with more than 1,000 views. For List of genes expressed in Brain and different tissues
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Public paired end chip seq dataset, both ChIP and input?
Popular Question 9 months ago, created a question with more than 1,000 views. For Difference between the Fasta files from UCSC and Gencode/Ensembl
Popular Question 11 months ago, created a question with more than 1,000 views. For Difference between the Fasta files from UCSC and Gencode/Ensembl
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Public paired end chip seq dataset, both ChIP and input?
Good Answer 17 months ago, created an answer that was upvoted at least 5 times. For A: Beginner in Bioinformatics / computational biology field
Student 17 months ago, asked a question with at least 3 up-votes. For Difference between the Fasta files from UCSC and Gencode/Ensembl
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Public paired end chip seq dataset, both ChIP and input?
Supporter 23 months ago, voted at least 25 times.
Appreciated 23 months ago, created a post with more than 5 votes. For A: Limma strange low p-values.
Good Answer 23 months ago, created an answer that was upvoted at least 5 times. For A: Beginner in Bioinformatics / computational biology field
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Public paired end chip seq dataset, both ChIP and input?
Scholar 23 months ago, created an answer that has been accepted. For A: Public paired end chip seq dataset, both ChIP and input?
Scholar 23 months ago, created an answer that has been accepted. For A: Public paired end chip seq dataset, both ChIP and input?
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Public paired end chip seq dataset, both ChIP and input?
Scholar 23 months ago, created an answer that has been accepted. For A: Public paired end chip seq dataset, both ChIP and input?
Scholar 23 months ago, created an answer that has been accepted. For A: Public paired end chip seq dataset, both ChIP and input?
Appreciated 23 months ago, created a post with more than 5 votes. For A: Limma strange low p-values.
Scholar 23 months ago, created an answer that has been accepted. For A: Public paired end chip seq dataset, both ChIP and input?
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Public paired end chip seq dataset, both ChIP and input?
Scholar 2.0 years ago, created an answer that has been accepted. For A: Public paired end chip seq dataset, both ChIP and input?
Teacher 2.0 years 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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