User: Arindam Ghosh
Arindam Ghosh • 150
- Reputation:
- 150
- Status:
- Trusted
- Location:
- India
- Website:
- https://ag1805x.github...
- Twitter:
- ag1805x
- Last seen:
- 3 days, 6 hours ago
- Joined:
- 3 years, 3 months ago
- Email:
- a******@outlook.in
I am currently working as a Junior Research Fellow at the Centre of Bioinformatics, University of Allahabad. I hold an undergraduate (B.Sc.) degree in Biotechnology from West Bengal University of Technology, India and a postgraduate (M.Sc.) degree in Bioinformatics from Alagappa University, India. My current research interests include stem cell bioinformatics, RNA-seq data analysis and network biology.
Posts by Arindam Ghosh
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... I need to extract the sample source for a list of sample ids. I tried using efetch as follows:
efetch -db biosample -id SAMN04383980 -format xml | xtract -pattern BioSampleSet -division BioSample -group Attributes -element Attribute
The problem here is that there are often more than two attri ...
written 10 days ago by
Arindam Ghosh • 150
• updated
10 days ago by
Pierre Lindenbaum ♦ 116k
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2
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... I have tried the approach 2 and as you mentioned the overlap is very less but to some extent has biological relevance. One major shortcoming of approach 2 is the number of replicates within each experiment. This now compels me to move towards approach 1.
Can you help me with some papers that have u ...
written 11 days ago by
Arindam Ghosh • 150
0
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1
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80
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... That's my concern. Even in their [example][1] problem in their [paper][2] I saw a similar situation.
[1]: https://www.ncbi.nlm.nih.gov/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=Click%20on%20image%20to%20zoom&p=PMC3&id=2995124_btq596f1.jpg
[2]: https://www.ncbi.nlm.n ...
written 16 days ago by
Arindam Ghosh • 150
2
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1
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80
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1
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... While clustering a network using Community Cluster (GLay) in ClusterMaker it gives a cluster number for each cluster. What does this represent?
I Initially thought it to simple numbers to distinguish between two clusters but I saw that the cluster with highest node is at #2 while the other major clu ...
written 18 days ago by
Arindam Ghosh • 150
• updated
16 days ago by
scooter • 80
0
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1
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190
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Comment:
C: How to construct GCN?
... But constructing only network with gene expression for single condition will give how the genes are correlated between the samples of a single condition. It won't tell much if any two genes are correlated across conditions.
Again, for any given condition the gene expression values should be same ac ...
written 7 weeks ago by
Arindam Ghosh • 150
2
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1
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190
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1
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... I have gene expression values for TEST and CONTROL samples from RNA-seq. I have determined the differentially expressed genes (DEG). Now I need to prepare a co-expression network of only the DEG. I did this by calculating the Pearson Correlation Coefficient (PCC) values using the corr.test() in R an ...
written 7 weeks ago by
Arindam Ghosh • 150
• updated
7 weeks ago by
Kevin Blighe ♦ 37k
0
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575
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Comment:
C: Low Sample For Coexpression
... Ok sorry. I missed to mention. 90% of the maximum possible correlation between n genes given by (n*(n-1))/2. ...
written 8 weeks ago by
Arindam Ghosh • 150
0
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0
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575
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Comment:
C: Low Sample For Coexpression
... A bit of clarification. While doing WGCNA or any other co-expression network, do we have to use the expression values for both the conditions of only a single condition?
I used Pearson Correlation Coefficients to create an unweighted network. Using 0.9 as threshold, I found that ~90% of interaction ...
written 8 weeks ago by
Arindam Ghosh • 150
0
votes
1
answer
653
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1
answers
... A bit of clarification. While doing WGCNA or any other co-expression network, do we have to use the expression values for both the conditions of only a single condition? ...
written 8 weeks ago by
Arindam Ghosh • 150
0
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2
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5.0k
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2
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Comment:
C: Questions about DAVID
... Which one is best suggested to annotate a set of up-regulated ges? ...
written 4 months ago by
Arindam Ghosh • 150
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