User: snamjoshi87

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snamjoshi8730
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Posts by snamjoshi87

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Comment: C: biomaRT GO-ID retreival showing different genes than AmiGO
... I just realized I never really specified in my question what output I wanted. If you run the code you have supplied above, you get the genes for all child terms. If you use multiple genes, you will get a combination of all child terms for all the parent GO terms you supplied which makes sense. But t ...
written 2.3 years ago by snamjoshi8730
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Comment: C: biomaRT GO-ID retreival showing different genes than AmiGO
... Sorry for the late response! This worked for me. Only thing to note is that if you pass multiple GO IDs to the values parameter it will not work the way I was intending in the question. Thanks! ...
written 2.3 years ago by snamjoshi8730
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biomaRT GO-ID retreival showing different genes than AmiGO
... I am trying to retrieve all genes that match a particular GO-ID using biomaRt: ensembl <- useMart("ensembl", dataset = "mmusculus_gene_ensembl") goGenes <- getBM(attributes = c("mgi_symbol", "go_id"),                  filters = "go_id",                  values = "GO:0098793",                 ...
go biomart written 2.5 years ago by snamjoshi8730 • updated 2.5 years ago by Mike Smith3.7k
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Is it possible to coerce dataframe to enrichResult class in clusterProfiler?
... I have some DAVID GO results that I have performed my own filtering on. I would like to now use the simplify() function from clusterProfiler to reduce redundancy as well as take advantage of some of the visualization tools in this package. However, the simplify() function only accepts enrichResult o ...
clusterprofiler written 2.5 years ago by snamjoshi8730 • updated 2.5 years ago by Guangchuang Yu1.1k
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Comment: C: Problem with getsequence() function in biomaRt
... This helped part of the way but then I was still getting an error! Turns out that the seqinr package (from CRAN) which I had loaded also has a getsequence() function and it was overriding the biomaRt one. ...
written 2.5 years ago by snamjoshi8730
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Problem with getsequence() function in biomaRt
... I've used this code before to get sequences but not it does not seem to work. I have updated Bioconductor and BiomaRt to their latest versions. When I run this code (where genes is a dataframe of one column with my genes of interest (official gene symbol): ensembl <- useMart("ensembl", dataset ...
biomart written 2.5 years ago by snamjoshi8730 • updated 2.5 years ago by James W. MacDonald50k
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Comment: C: Multi-way interaction design in limma
... Wow, okay so your example made me understanding contrasts. It really is a lot simpler than I have been making it out to be (which is why you keep saying "literally"!). Alright, thanks for your suggestions, this has been really helpful. I think I am finally getting the hang of it.   ...
written 2.6 years ago by snamjoshi8730
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Comment: C: Multi-way interaction design in limma
... No, it's clear. I am working with multiple software at the same time and I think I mistakenly read something from a different documentation. Sorry about that. I will modify my question so I don't confuse anyone else who reads it. ...
written 2.6 years ago by snamjoshi8730
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Comment: C: Multi-way interaction design in limma
... Yes, I think so! Thank you so much! So after making the contrast matrix, I can do something like: fit <- lmFit(logCPM, design) fitCont <- contrasts.fit(fit, contrast) fitCont <- eBayes(fitCont) results <- topTable(fitCont) What I see in the "logFC" column should be the fold change of ...
written 2.6 years ago by snamjoshi8730
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Multi-way interaction design in limma
... Hello, I am having a lot of difficulty setting up my design matrix. I have been searching extensively online for an answer but I think I lack some of the background to understand how to do this since my experiment is fairly complicated. I think I have a basic grasp of setting up model matrices in si ...
limma design matrix written 2.6 years ago by snamjoshi8730

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