User: ag1805x

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ag1805x20
Reputation:
20
Status:
New User
Location:
University of Allahabad
Website:
http://ag1805x.github.io/
Twitter:
ag1805x
Last seen:
14 hours ago
Joined:
1 year, 8 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. Open to opportunities in Environmental Genomics.

Posts by ag1805x

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Difference in PCA variance calculation in DESeq2
... Actually my aim was to see if after batch effect removal the samples clustered as desired according to the two sample types. As can be seen from the hclust results and from PCA 63% variance is explained by PC1. So I guess the job has been correctly done. ...
written 29 days ago by ag1805x20
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Comment: C: Difference in PCA variance calculation in DESeq2
... Thank you Mike. So it performs PCA on the top 500 genes by variance. Can you help me with the second part of the question: > Further, through hierarchical clustering, I observed two major clusters, but in these PCA I think there are three groups. ...
written 29 days ago by ag1805x20
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Difference in PCA variance calculation in DESeq2
... I was trying to plot PCA using DESeq2 `plotPCA` function and `prcomp` function. However, the variances I obtained was quite different. Why is this? ![prcomp PCA][1] ![DESeq2 PCA][2] **Code for PCA using prcomp:** pca <- prcomp(t(countsPC_batch)) percentage <- round(((pca$sdev^2) ...
deseq2 hclust pca written 29 days ago by ag1805x20 • updated 29 days ago by Michael Love26k
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Comment: C: tximport transcript missing
... Instead of generating the tx2gene file from GTF file or ensembldb, why not generate it from the reference transcriptome from which the index was generated. I encountered the same missing transcript problem while working with kallisto and this is a probable solution I found. https://gist.github.com ...
written 8 weeks ago by ag1805x20
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Design for introducing batch effect in DESeq2
... I have RNAseq data taken from two different ENA project IDs (PrjA & PrjB). Both PrjA & PrjB contains test and control samples. PrjA was PE 50bp sequencing while PrjB was SE 100bp. Is it possible we can combine the data to identify DEG between test and control? Would batch effect removal by C ...
edger deseq2 combat rna-seq batch effect written 11 weeks ago by ag1805x20 • updated 11 weeks ago by swbarnes2340
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How to arrange multiple plots into one page in NOISeq?
... I am using NOISeq to generate Biodetection plot. I have 6 samples and need to place the plots for each sample side by side for easy comparison. As per the manual, it seems I can only visualise two at a time. Is there a way to arrange all the six plots in 2 columns and 3 rows. I tried the code: ...
noiseq rna-seq quality control written 11 weeks ago by ag1805x20
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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 6 months ago by ag1805x20
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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 6 months ago by ag1805x20 • updated 6 months ago by Peter Langfelder2.3k
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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 13 months ago by ag1805x20
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Comment: C: log2FoldChange calculation in DESeq2 output
... When calculating fold change how is the reference group determined? ...
written 16 months ago by ag1805x20

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