User: adam.faranda

gravatar for adam.faranda
adam.faranda10
Reputation:
10
Status:
New User
Location:
Last seen:
2 weeks, 3 days ago
Joined:
3 years ago
Email:
a***********@gmail.com

Posts by adam.faranda

<prev • 10 results • page 1 of 1 • next >
0
votes
0
answers
145
views
0
answers
Duplicates in Biomart Query, Ensembl ID maps to multiple Entrez genes.
... When I run the following query on "ENSMUSG00000001175", I retrieve records for 2 corresponding entrezgene_id's (Calm1 and Calm2). The first record is correct, however the second record, "12314" is actually Calm2. annot<-getBM( attributes = c( "ensembl_gene_id", "entrezgene_i ...
ncbi ensembl biomart written 6 weeks ago by adam.faranda10 • updated 11 days ago by Biostar ♦♦ 20
0
votes
3
answers
171
views
3
answers
Comment: C: PCA on RNAseq time series data
... Hi @swbarnes2 -- I'm working on a similar type of project as the OP; but I still have a lot to learn about mitigating batch effects. If you include the batch covariate as a factor in the model design matrix, is that sufficient? I'm also wondering how you might apply to cluster analysis. Is there a ...
written 8 weeks ago by adam.faranda10
0
votes
3
answers
171
views
3
answers
Comment: C: PCA on RNAseq time series data
... Yes, sorry. The code I posted was a snippet from a larger function -- in order to plot samples, the matrix should be transposed such that rows are samples and columns are genes. pca<-prcomp( t(df), scale=T) p<-autoplot(pca, data = ft, colour=groupCol) p ...
written 8 weeks ago by adam.faranda10
0
votes
3
answers
171
views
3
answers
Answer: A: PCA on RNAseq time series data
... In R, I typically use the 'prcomp' function to evaluate principle components in "sample by gene" expression matrices. The object returned by this function can be passed directly to plotting functions. I would recommend the "autoplot" function from the package "ggfortify". Depending on whether you ...
written 8 weeks ago by adam.faranda10
0
votes
0
answers
92
views
0
answers
Best Methods for Measuring the similarity of two pairwise Gene Expression contrasts
... In a recent RNA Sequencing experiment, we've identified a set of genes with Pax6 dependent differential expression in the cornea. Initial evaluation of this signature suggests that in Pax6 mutants, corneal tissues begin to adopt a conjunctival phenotype. We've found an existing data set that provi ...
microarray rna-seq differential expression written 8 weeks ago by adam.faranda10
0
votes
0
answers
123
views
0
answers
Comment: C: Analyze normalized illumina microarray data
... I'm not sure that this "normalized" data is good for Limma Analyses yet. The "background normalization" method in BeadStudio can introduce negative values[1], which seems to be the case in the OP's data set. I found the paper below to be very helpful when trying to analyze illumina data using the " ...
written 8 weeks ago by adam.faranda10
0
votes
2
answers
232
views
2
answers
Answer: A: Mysterious genes in my Biomart results (genes that were not part of original que
... Thank you both for your prompt responses. Mike's answer was correct -- this appears to have been an issue with capitalization. > "SPATA24" doesn't look like a normal MGI symbol since it's all in caps, so I wouldn't be suprised if your query contains "Spata24" and the all caps version is ret ...
written 5 months ago by adam.faranda10
2
votes
2
answers
232
views
2
answers
Mysterious genes in my Biomart results (genes that were not part of original query)
... I'm using the R package 'biomaRt' to retrieve ensembl ID's and descriptions for a list of gene symbols (eg "Sf1", "Rhox7a" etc. . . ). My query consists of 41203 symbols; biomart returns a result set with 30774 records corresponding to the gene symbols recognized by ensembl. The 30774 records ret ...
R biomart package('biomart') written 5 months ago by adam.faranda10
2
votes
1
answer
256
views
1
answer
why does my biomaRt query return inconsistent dataset lists?
... I have been using the biomaRt library to retrieve ensembl gene ID's for mouse genes. This moring, I got an unusual error message when running a previously validated script: mart <- useMart(biomart="ensembl", dataset="mmusculus_gene_ensembl") Error in useDataset(mart = mart, dataset = da ...
ensembl biomart R written 6 months ago by adam.faranda10
0
votes
0
answers
750
views
0
answers
DAVID Web Services, Perl Client troubleshooting
... DAVID provides a web service for automating enrichment analysis. In connection they've made available a set of example clients. I'm having some difficulty getting one of the perl clients to work, and was hoping that someone on BioStars was familiar with this tool. When I try and run the tableRepo ...
software error perl david soap written 3.0 years ago by adam.faranda10

Latest awards to adam.faranda

Scholar 5 months ago, created an answer that has been accepted. For A: Mysterious genes in my Biomart results (genes that were not part of original que

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2013 users visited in the last hour