User: brianj.park

gravatar for brianj.park
brianj.park50
Reputation:
50
Status:
Trusted
Location:
Montréal, Canada
Last seen:
1 day, 5 hours ago
Joined:
3 years, 6 months ago
Email:
b**********@mail.utoronto.ca

Posts by brianj.park

<prev • 13 results • page 1 of 2 • next >
0
votes
1
answer
69
views
1
answers
Answer: A: EdgeR normalization doesn't change gene count number
... You are not using discrete read counts for differential expression. There is a function called `cpm` that transforms your data into continuous log scale and you use these values for downstream differential expression. If you run `lcpm <- cpm(y, log=TRUE)` and `lcpm <- cpm(ynorm, log=TRUE)` you ...
written 11 days ago by brianj.park50
2
votes
2
answers
274
views
2
answers
Answer: A: Comparing gene ontology for two lists of genes
... You could give clusterProfiler a shot using `compareCluster()`. You'd need to prepare a data frame where each column is a gene list and then do something like: require(clusterProfiler) require(enrichplot) require(org.Hs.eg.db) cluster <- compareCluster(geneClusters = df, fun = " ...
written 5 months ago by brianj.park50
1
vote
1
answer
167
views
1
answers
Answer: A: Differential gene expression help
... Your design matrix made with `model.matrix()` needs to have the same number of rows as the columns in your count table (i.e., the number of your samples). It'd help if you posted your code and examples. ...
written 5 months ago by brianj.park50
0
votes
2
answers
234
views
2
answers
Answer: A: Bioinformatics: Converting Protein Refseq ID to Entrez Gene Accession
... You can use [org.Mm.eg.db][1]. library(org.Mm.eg.db) Mm <- org.Mm.eg.db my_symbol <- "NP_001229937" select(mm, keys = my_symbol, columns = c("REFSEQ", "ENSEMBL"), keytype = "REFSEQ") REFSEQ ENSEMBL 1 NP_001229937 ENSMUSG00000048126 [1]: https://bioc ...
written 6 months ago by brianj.park50
0
votes
0
answers
186
views
0
answers
Comment: C: small RNA seq data from human cell line only give me 0 counts
... is there a chance you entered the wrong strand orientation for your reads? Specifically it's the `--stranded` option when you run htseq-count. ...
written 6 months ago by brianj.park50
0
votes
4
answers
1.7k
views
4
answers
Comment: C: Compare sets of GO enrichments
... Do you mean you want a database of gene sets? Above graph is using Gene Ontology (GO) database to associate related genes by their function (i.e., BP, MF, CC). http://geneontology.org/ You may also use KEGG which is divided into 7 broad categories of biochemical processes: https://www.genome.jp/keg ...
written 7 months ago by brianj.park50
0
votes
4
answers
1.7k
views
4
answers
Comment: C: Compare sets of GO enrichments
... You need a data frame in which the columns correspond to a list of gene identifiers. Check the vignette for clusterProfiler, specifically chapter 11. https://yulab-smu.github.io/clusterProfiler-book/chapter11.html ...
written 7 months ago by brianj.park50
0
votes
1
answer
971
views
1
answers
Comment: A: ERROR: failed to find the gene identifier attribute in the 9th column of the pro
... Have you looked at the contents of your provided GTF file? With the `-g` option on featureCounts you're telling it to look for the identifier you proided. Most likely your GTF file is either missing the identifier you provided or is using a different name. ...
written 7 months ago by brianj.park50
1
vote
1
answer
277
views
1
answers
Answer: A: RNA_Seq Data Analyse
... After you imported your count table into R, you have to create a DGEList object that contains your counts, gene IDs, and sample group info needed for differential expression. Follow [this vigenette][1] and it should be straightforward. [1]: https://bioconductor.org/packages/release/workflows/v ...
written 9 months ago by brianj.park50
1
vote
2
answers
262
views
2
answers
Answer: A: Downstream RNA seq analysis
... You could take the list of differentially expressed genes and their p-values to do some gene ontology enrichment analysis. [TopGO][1] is a useful tool on R for that. [1]: https://bioconductor.org/packages/release/bioc/html/topGO.html ...
written 9 months ago by brianj.park50

Latest awards to brianj.park

Scholar 5 months ago, created an answer that has been accepted. For A: Comparing gene ontology for two lists of genes

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1442 users visited in the last hour