User: ag1805x

gravatar for ag1805x
ag1805x10
Reputation:
10
Status:
New User
Location:
University of Allahabad
Website:
http://ag1805x.github.io/
Twitter:
ag1805x
Last seen:
2 weeks, 6 days ago
Joined:
1 year, 2 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 ag1805x

<prev • 12 results • page 1 of 2 • next >
0
votes
1
answer
54
views
1
answers
Comment: C: WGCNA from different lengths RNAseq read
... Before we can apply VST in DESeq2 we have to normalize the data. Now Performing VST separately would mean normalizing data separately. Would that be good? > Success is by no means guaranteed, but it's worth a try. How do I judge success? Any parameter you would suggest. ...
written 20 days ago by ag1805x10
1
vote
1
answer
54
views
1
answer
WGCNA from different lengths RNAseq read
... Is it advisable to create WGCN from RNA-seq data generated on different platforms with different read lengths but processed the same way? Suppose I have 3 datasets with each containing 5 CASE and 5 CONTROL samples. ...
rnaseq network wgcna co-expression written 21 days ago by ag1805x10 • updated 21 days ago by Peter Langfelder1.9k
0
votes
2
answers
8.3k
views
2
answers
Comment: C: DESeq2 FPKM normalization
... So if we need to compare between two sets of data from two different experiments, is it worth using COMBAT to remove batch effect and then use edgeR to normalize by TPM and DE analysis? ...
written 7 months ago by ag1805x10
0
votes
1
answer
5.6k
views
1
answers
Comment: C: log2FoldChange calculation in DESeq2 output
... When calculating fold change how is the reference group determined? ...
written 10 months ago by ag1805x10
0
votes
1
answer
2.5k
views
1
answers
Comment: C: "Over-correction" in the size-factors of the DESeq2 package
... What is a good range for size factors? In the manual I saw it should be near to 1. How much can it vary?  ...
written 10 months ago by ag1805x10
0
votes
2
answers
183
views
2
answers
What are the different strategies to filter out low count genes?
... What are the different strategies to filter low count genes? Some of the ones I have seen in different papers are: rowSums(count)>0 rowVariance(count)>1 ...
rnaseq deseq2 differential gene expression written 10 months ago by ag1805x10 • updated 10 months ago by Wolfgang Huber13k
0
votes
1
answer
3.6k
views
1
answers
Comment: C: Too many (?) differentially expressed genes - edgeR and DESeq
... Hi Darya, I am working with something similar. Even I found about 49% of the ~20k protein Coding genes to be deferentially expressed. If you could share how you dealt with this or justified the observation. ...
written 10 months ago by ag1805x10
0
votes
2
answers
2.1k
views
2
answers
Comment: C: DESeq2 vs Ballgown results
... Same problem with my data. Huge difference between DEG reported by Ballgown and DESeq2. I have now shifted from Hisat2>Stringtie>Ballgown to using Hisat2>FeatureCounts>DESeq2. Is this combination good? ...
written 10 months ago by ag1805x10
0
votes
2
answers
3.7k
views
2
answers
Comment: C: Ballgown up and down regulated genes
... How many replicated do you have per group? I had similar problem when I had 2 replicates per group; but increasing it to 3 solved the problem.  ...
written 14 months ago by ag1805x10
1
vote
2
answers
1.3k
views
2
answers
Comment: C: How fold change is calculated in Ballgown?
... Is any log transformation done on the FPKM values during FC calculation? I tried to manually calculate the FC by extracting the FPKM values for few genes using gexpr(), but the result I obtained differs considerably from the stattest result. Also after stattest the genes that were supposed to be up ...
written 14 months ago by ag1805x10

Latest awards to ag1805x

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 129 users visited in the last hour