All Questions
Tagged with gene bioconductor
7 questions
3
votes
1
answer
456
views
What is it about gene names starting with "LOC"?
I was struggling to use AnnotationDbi to change my ensemble ID to gene name, for datasets of three different species (human, canine, mouse). Among gene names for all three species there are genes with ...
- 69
1
vote
1
answer
75
views
Gene ensemble vs Hugo id
Hi
I have been recently struggling with the gene annotations and changing gene ID to ensemble ID. While I was doing that there were some genes for the same species that had the same gene ID but ...
- 69
1
vote
1
answer
600
views
Retrieving all genes for a gene ontology term
I'm looking for an easy way to retrieve all the genes in a list that are associated with a certain GO term, preferably using R/Bioconductor packages. I'm not interested in under/overrepresentation or ...
- 11
0
votes
3
answers
770
views
How to find correlation between two specific genes in same dataset?
I would like to plot the correlation between two specific genes in my data. I have a matrix with genes in rows and samples in columns, with read counts data. If I want to look at the correlation ...
- 631
9
votes
3
answers
3k
views
How to identify gene expression signatures from gene expression data?
I have TCGA gene expression data. I'm interested in identifying gene expression signatures using the data.
I would like to know whether there are any tools or R packages for identifying gene ...
- 1,272
2
votes
2
answers
79
views
When working with Bioconductor and the curatedOvarianData dataset, what are the unit values of the expression data?
I am wondering how to interpret values inside the gene expression levels contained within Bioconductor. For example, if we have the following commands via R, we get:...
- 121
8
votes
2
answers
86
views
Melt p-values for CpG sites mapping to the same gene
I have some data I am working with, and I am curious if I am able to combine p-values from a paired t-test for CpG sites in the genome using Fisher's Method to get one p-value for each unique gene. ...
- 81