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User: adam.faranda

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adam.faranda • 10
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Posts by adam.faranda

<prev • 10 results • page 1 of 1 • next >
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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.faranda • 10 • updated 11 days ago by Biostar ♦♦ 20
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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.faranda • 10
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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.faranda • 10
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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.faranda • 10
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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.faranda • 10
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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.faranda • 10
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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.faranda • 10
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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.faranda • 10
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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.faranda • 10
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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.faranda • 10

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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
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