User: kaushal Raj Chaudhary

Reputation:
10
Status:
New User
Location:
United States
Last seen:
4 years, 5 months ago
Joined:
6 years ago
Email:
k**********@gmail.com

Posts by kaushal Raj Chaudhary

<prev • 23 results • page 1 of 3 • next >
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Journal articles for whole exome sequencing
... Hello Forum, I am new to whole exome sequencing and I was looking for best articles to know more  in depth about it .  Would you recommend any articles?  Thank you for kind help in advance. ...
exomecopy exon array analysis codex written 4.5 years ago by kaushal Raj Chaudhary10
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Comment: C: Analyzing gene expression data( not celfiles) in limma and annotating results
... Hi Jim, How can I remove duplicate probe ids before fitting in lmfit ( not in MArrayLM object)? Your code removes the duplicates only after fitting the model.    Thanks !!! gns <- gns[!duplicated(gns[,1]),] fit2$genes <- gns topTable(fit2,2) ...
written 4.6 years ago by kaushal Raj Chaudhary10
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Comment: C: Analyzing gene expression data( not celfiles) in limma and annotating results
... Hi Steve, Thank you for help. Yes, expression values are log2 transformed.  Now I suppose I can merge annotation table and  results from toptable(). ...
written 4.6 years ago by kaushal Raj Chaudhary10
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Analyzing gene expression data( not celfiles) in limma and annotating results
... I have gene expression data (not image files) obtained from affymetrix chip and I used limma to analyze it.  The row names of top table does not match the probe id. I saw this thread for annotating results from celfiles (https://support.bioconductor.org/p/63834/).  I wonder how can I annotate the r ...
annotation limma written 4.6 years ago by kaushal Raj Chaudhary10 • updated 4.6 years ago by Steve Lianoglou12k
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Comment: C: Gene set enrichment analysis
... Thanks Jim.   ...
written 4.9 years ago by kaushal Raj Chaudhary10
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Comment: C: Gene set enrichment analysis
... Hi Jim, How did you come up with that genes?  Can I use those gene list  in index argument of geneSetTest() function?   Thank you. ...
written 4.9 years ago by kaushal Raj Chaudhary10
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Comment: C: Gene set enrichment analysis
... Hi Steve, It does not seem they have rat genes. How to map rat genes to human genes or mouse genes so I can use it geneSetTest() function? Thanks !!! ...
written 4.9 years ago by kaushal Raj Chaudhary10
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Comment: C: Gene set enrichment analysis
... Hi Jim, I  am mostly interested in PI3K/AKT singnaling pathway.  Would that be a gene set than can be tested against background?  I don't have any other known gene set that I can test. Thanks !!! ...
written 4.9 years ago by kaushal Raj Chaudhary10
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Comment: C: Gene set enrichment analysis
... Thanks Jim !!! ...
written 4.9 years ago by kaushal Raj Chaudhary10

Latest awards to kaushal Raj Chaudhary

Popular Question 4.5 years ago, created a question with more than 1,000 views. For Gene set enrichment analysis
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Gene set enrichment analysis

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