User: Brian Smith

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Brian Smith90
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9 months ago
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4 years, 1 month ago
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Posts by Brian Smith

<prev • 47 results • page 1 of 5 • next >
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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 9 months ago by Brian Smith90 • updated 8 months ago by Wade Davis0
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Answer: A: SAM/siggenes: Differential gene expression analysis
... Thanks James! ...
written 10 months ago by Brian Smith90
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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 10 months ago by Brian Smith90
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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 12 months ago by Brian Smith90
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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 12 months ago by Brian Smith90
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Comment: C: Gviz issue: crashing when AnnotationTrack( ... , just.group="above")
... d'oh! My mistake!  ...
written 15 months ago by Brian Smith90
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Comment: C: Gviz issue: crashing when AnnotationTrack( ... , just.group="above")
... I do have 7 tracks - is that too many? It works fine if I leave off the knownGenes track. I get the same error even if I increase the pdf size: pdf(file='test_plot.pdf',onefile=T,width=14,length=14) The gene track is for the region chr20:58887626-58892145     ...
written 15 months ago by Brian Smith90
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Answer: A: Gviz issue: crashing when AnnotationTrack( ... , just.group="above")
... Hi Florian, I am getting the same error. The bioconductor website still appears to have Gviz 1.16.1 (https://bioconductor.org/packages/release/bioc/html/Gviz.html). How can I get release 1.16.3? My error is:  Error in .local(GdObject, ...) :    Too many stacks to draw. Either increase the device ...
written 15 months ago by Brian Smith90
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org.Hs.eg.db - hg38 build?
... Hi, How can I determine which build org.Hs.eg.db based on?   thanks! ...
org.hs.eg.db written 16 months ago by Brian Smith90 • updated 16 months ago by Keith Hughitt90
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illumina methylationEPIC 850k array
... Hi, Just wondering if anyone has yet looked at some 850k data, and whether existing packages (e.g. minfi) can be readily applied to get the methylation data. Not too many publications yet, but there seems to be a dataset in GEO... thanks! ...
illumina methylationepic 450k written 21 months ago by Brian Smith90

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Popular Question 20 months ago, created a question with more than 1,000 views. For BiomaRt: protein coding transcript identification
Popular Question 20 months ago, created a question with more than 1,000 views. For topGO: How to create gene2GO annotation for mouse?

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