User: Ar

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Ar810
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810
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United States
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https://www.linkedin.c...
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aayushraman
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3 days, 1 hour ago
Joined:
3 years, 10 months 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 21 months ago by Ar810
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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 2.5 years ago by Ar810
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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 2.5 years ago by Ar810
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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 2.5 years ago by Ar810
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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 2.5 years ago by Ar810
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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 2.5 years ago by Ar810
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Comment: C: Difference between the Fasta files from UCSC and Gencode/Ensembl
... Thanks a lot. That was helpful! ...
written 2.6 years ago by Ar810
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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 2.6 years ago by Ar810
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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 2.6 years ago by Ar810
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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 2.6 years ago by Ar810

Latest awards to Ar

Appreciated 7 months ago, created a post with more than 5 votes. For A: Beginner in Bioinformatics / computational biology field
Good Question 7 months ago, asked a question that was upvoted at least 5 times. For Difference between the Fasta files from UCSC and Gencode/Ensembl
Popular Question 7 months ago, created a question with more than 1,000 views. For List of genes expressed in Brain and different tissues
Appreciated 8 months ago, created a post with more than 5 votes. For A: Beginner in Bioinformatics / computational biology field
Popular Question 12 months ago, created a question with more than 1,000 views. For List of genes expressed in Brain and different tissues
Scholar 12 months ago, created an answer that has been accepted. For A: Public paired end chip seq dataset, both ChIP and input?
Teacher 12 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 13 months ago, created a question with more than 1,000 views. For List of genes expressed in Brain and different tissues
Teacher 19 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 19 months ago, created a question with more than 1,000 views. For Difference between the Fasta files from UCSC and Gencode/Ensembl
Popular Question 21 months ago, created a question with more than 1,000 views. For Difference between the Fasta files from UCSC and Gencode/Ensembl
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Public paired end chip seq dataset, both ChIP and input?
Good Answer 2.2 years ago, created an answer that was upvoted at least 5 times. For A: Beginner in Bioinformatics / computational biology field
Student 2.2 years ago, asked a question with at least 3 up-votes. For Difference between the Fasta files from UCSC and Gencode/Ensembl
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Public paired end chip seq dataset, both ChIP and input?
Supporter 2.7 years ago, voted at least 25 times.
Appreciated 2.7 years ago, created a post with more than 5 votes. For A: Limma strange low p-values.
Good Answer 2.7 years ago, created an answer that was upvoted at least 5 times. For A: Beginner in Bioinformatics / computational biology field
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Public paired end chip seq dataset, both ChIP and input?
Scholar 2.8 years ago, created an answer that has been accepted. For A: Public paired end chip seq dataset, both ChIP and input?
Scholar 2.8 years ago, created an answer that has been accepted. For A: Public paired end chip seq dataset, both ChIP and input?
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Public paired end chip seq dataset, both ChIP and input?
Scholar 2.8 years ago, created an answer that has been accepted. For A: Public paired end chip seq dataset, both ChIP and input?
Scholar 2.8 years ago, created an answer that has been accepted. For A: Public paired end chip seq dataset, both ChIP and input?
Appreciated 2.8 years ago, created a post with more than 5 votes. For A: Limma strange low p-values.

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