User: Brian Smith

gravatar for Brian Smith
Brian Smith120
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120
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United States
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5 hours ago
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4 years, 8 months ago
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b***********@gmail.com

Posts by Brian Smith

<prev • 54 results • page 1 of 6 • next >
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Comment: C: Biostrings: "Error in .normargSEW(start, "start")"
... D'oh..!! Thanks!! ...
written 4 days ago by Brian Smith120
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Biostrings: "Error in .normargSEW(start, "start")"
... Hi, I was getting an error with a simple Biostring function. Here is the code, error and session info. Am I using some outdated package? many thanks! ====================== > library(Biostrings) > > tdna <- DNAString("TGCGATGCGCACG") > print(tdna) 13-letter "DNAString" instanc ...
biostrings written 4 days ago by Brian Smith120 • updated 4 days ago by Martin Morgan ♦♦ 21k
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genes in rhesus genome (ref. TxDb.Mmulatta.UCSC.rheMac8.refGene)
... Hi, I was trying to do some comparative analysis between the rhesus and human genes. I seem to get no genes that are common to both species! What am I doing wrong? My code, screen output :   ============= library("TxDb.Hsapiens.UCSC.hg38.knownGene") library("org.Hs.eg.db") library("TxDb.Mmulatt ...
org.hs.eg.db org.mmu.eg.db written 8 weeks ago by Brian Smith120 • updated 8 weeks ago by James W. MacDonald46k
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Comment: C: RNA-Seq : zero counts
... Thanks thokall. You were right! ...
written 6 months ago by Brian Smith120
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Comment: C: RNA-Seq : zero counts
... ah, I now see what the error message was trying to tell me! James, thanks for all your help!! ...
written 6 months ago by Brian Smith120
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Comment: C: RNA-Seq : zero counts
... Hi James, Thanks for the reply. Yep, you were right - checking back, it was aligned using UCSC while I was trying with ensembl.  As per your suggestion above, I tried using UCSC but get a new error:   > ebg <- exonsBy(TxDb.Hsapiens.UCSC.hg38.knownGene, by="gene") > bamfiles <- BamFi ...
written 6 months ago by Brian Smith120
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RNA-Seq : zero counts
... Hi, This is my first time with RNA-Seq analysis, so I might be doing something wrong! I got some bam files from a collaborator that I need to process. I followed the pipeline, but I seem to be getting 0 counts! The warnings given are "The 2 combined objects have no sequence levels in common." What ...
rnaseq bioconductor written 6 months ago by Brian Smith120 • updated 6 months ago by James W. MacDonald46k
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Epigenetic clock (Horvath): package?
... Hi, I was working with some illumina EPIC data and trying to determine the epigenetic age of samples for whole blood. I know that on Horvath's website there is an online calculator for whole blood, but the code doesn't seem to be provided. Also, in the vignette for minfi, in section "Other stuff" t ...
epigenetics minfi methylation illimina 450k methylation written 16 months ago by Brian Smith120 • updated 15 months ago by Wade Davis60
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Answer: A: SAM/siggenes: Differential gene expression analysis
... Thanks James! ...
written 17 months ago by Brian Smith120
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SAM/siggenes: Differential gene expression analysis
... Hi, I was trying to do a Significance Analysis of Microarray data for some data (~20,000 genes x 8 total samples). My samples (n=4) belong to either of two groups (A and B). I have two replicates for each sample. So, my samples are: Sample1_A_replicate1 Sample2_B_replicate1 Sample3_A_replicate1 Sa ...
microarray siggenes sam gene expression written 17 months ago by Brian Smith120

Latest awards to Brian Smith

Popular Question 16 months ago, created a question with more than 1,000 views. For org.Hs.eg.db - convert ALIAS to ENTREZID, GENENAME
Popular Question 16 months ago, created a question with more than 1,000 views. For BiomaRt: protein coding transcript identification
Popular Question 16 months ago, created a question with more than 1,000 views. For topGO: genes annotated to a significant GO term
Student 16 months ago, asked a question with at least 3 up-votes. For Chromosome position to nucleotide - Biostrings?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For BiomaRt: protein coding transcript identification
Popular Question 2.3 years ago, created a question with more than 1,000 views. For topGO: How to create gene2GO annotation for mouse?

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