User: GENOMIC_region

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Posts by GENOMIC_region

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Filtering probesets for HuEx ST1.0 after probeset normalization
... Hi all,   I'm working with exon level microarray analysis. I've two annotation files - probeset and transcripts. I normalize data on two targets - gene and probesets to get estimates at gene level and exon level respectively.    After filtering genes that aren't in probeset annotation and probeset ...
microarray exons probefiltering written 5 days ago by GENOMIC_region0
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Comment: C: Map exon level probeset to gene level probeset - Huex ST1.0
... Thank you very much. :) ...
written 5 days ago by GENOMIC_region0
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Map exon level probeset to gene level probeset - Huex ST1.0
... Hi all,   I've HuEx ST1.0 microarray data. Using Oligo package I get gene level expression (RMA, target=core) and for exon probes I get expression using RMA (target = probeset).    I'd like to map the probesets from exon level expression to genes.  I've HuEx-1_0-st-v2.na36.hg19.transcript.csv and ...
exon array analysis pd.huex.1.0.st.v2 written 7 days ago by GENOMIC_region0 • updated 6 days ago by James W. MacDonald48k
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Comment: C: Human Exon: arome.affymetrix residuals Inf value
... Ah, thank you. ...
written 11 days ago by GENOMIC_region0
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Human Exon: arome.affymetrix residuals Inf value
... Hello all, I'm working HuEx ST 1.0 microarray data. Trying to get estimates for exon and transcript level, plot residuals. In the code below I perform RMA for exons. In the end I get a data frame, which looks OK. Code and steps from http://www.aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysi ...
exon array analysis exons written 12 days ago by GENOMIC_region0 • updated 12 days ago by James W. MacDonald48k
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Answer: A: comparing 2 long BED files in R in an efficient way
... Cross posted: https://www.biostars.org/p/324164/ ...
written 4 months ago by GENOMIC_region0
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GWAS: access Imputation probabilities: snpStats
... Hi there, I'm interested to work with .gen file generated from IMPUTE2 imputation tool. In particular I need probabilities per SNP. I use snpStats' function: test_impute<-read.impute("genotyped_snps_chr22.impute", rownames = NULL, nsnp = NULL, snpcol = 2) But the output I get is snpMatrix, wh ...
snpstats gwas imputation written 4 months ago by GENOMIC_region0
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Comment: C: IRanges which are not S4 generic: endoapply mendoapply error in loading oligocla
... Thank you for your reply. That helps; I'd to downgrade certain packages that were too new for Bioconductor version '3.6'.  ...
written 4 months ago by GENOMIC_region0
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IRanges which are not S4 generic: endoapply mendoapply error in loading oligoclasses
... I'm having issues for loading libraries: Step1: library("oligo",lib.loc="~/R_LIB") library("pd.huex.1.0.st.v2",lib.loc="~/R_LIB") Error: Loading required package: IRanges Error: package or namespace load failed for ‘IRanges’:  Functions found when exporting methods from the namespace ‘IRanges’ ...
oligoclasses iranges biocgenerics written 4 months ago by GENOMIC_region0
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Comment: C: GENESIS: PCAIR: Error in acc(object, NL[cnode]) : unmatched node provided
... Thank you so so much for digging into this. :) ...
written 5 months ago by GENOMIC_region0

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