User: Brian Smith

gravatar for Brian Smith
Brian Smith110
Reputation:
110
Status:
Trusted
Location:
United States
Last seen:
2 months, 2 weeks ago
Joined:
4 years, 4 months ago
Email:
b***********@gmail.com

Posts by Brian Smith

<prev • 51 results • page 1 of 6 • next >
0
votes
1
answers
237
views
1
answers
Comment: C: RNA-Seq : zero counts
... Thanks thokall. You were right! ...
written 11 weeks ago by Brian Smith110
0
votes
1
answers
237
views
1
answers
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 11 weeks ago by Brian Smith110
0
votes
1
answers
237
views
1
answers
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 11 weeks ago by Brian Smith110
4
votes
1
answer
237
views
1
answer
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 11 weeks ago by Brian Smith110 • updated 11 weeks ago by James W. MacDonald45k
0
votes
1
answer
431
views
1
answer
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 12 months ago by Brian Smith110 • updated 11 months ago by Wade Davis60
0
votes
2
answers
245
views
2
answers
Answer: A: SAM/siggenes: Differential gene expression analysis
... Thanks James! ...
written 13 months ago by Brian Smith110
2
votes
2
answers
245
views
2
answers
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 13 months ago by Brian Smith110
0
votes
2
answers
323
views
2
answers
Answer: A: metagenomeSeq: cumNormStat normalization default
... Hi Joseph, Thanks! That worked. Sorry for very basic questions - just got started on microbiome. I used silva and mothur to get my OTUs. However, I get something like : ========= > yy <- aggTax(myobj, lvl = "phylum", out = "MRexperiment") > MRcounts(yy)[1:5,1:5] sample_4 sample_5 sampl ...
written 15 months ago by Brian Smith110
0
votes
2
answers
323
views
2
answers
metagenomeSeq: cumNormStat normalization default
... Hi, I was trying to normalize my count/reads data using cumNormStat function. The code executes with the 'default value', and doesn't appear to change the count values after the normalization. Am I doing something wrong? Or is the 'default value' the most appropriate value for my dataset?   > ...
microbiome metagenomeseq written 15 months ago by Brian Smith110
0
votes
3
answers
783
views
3
answers
Comment: C: Gviz issue: crashing when AnnotationTrack( ... , just.group="above")
... d'oh! My mistake!  ...
written 18 months ago by Brian Smith110

Latest awards to Brian Smith

Popular Question 23 months ago, created a question with more than 1,000 views. For BiomaRt: protein coding transcript identification
Popular Question 23 months ago, created a question with more than 1,000 views. For topGO: How to create gene2GO annotation for mouse?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 371 users visited in the last hour