User: GENOMIC_region

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Posts by GENOMIC_region

<prev • 18 results • page 1 of 2 • next >
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Comment: C: WGCNA: cleaning for sample outliers
... Hi Lluis,   Thank you very much. That helps. :) ...
written 10 weeks ago by GENOMIC_region0
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WGCNA: cleaning for sample outliers
... Hi there,   I'm working with 363 samples with 10K genes. My workflow is: load data, transpose, get gene names. use hclust. Plot data once and see where abline has to be drawn. I draw plot for clustering with eye-balled abline. I'm lost with cutheight and min size while cleaning samples. Below are ...
microarray wgcna gene network written 10 weeks ago by GENOMIC_region0 • updated 9 weeks ago by Bioconductor Community ♦♦ 0
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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 4 months 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 4 months 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 4 months ago by GENOMIC_region0 • updated 4 months ago by James W. MacDonald49k
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Comment: C: Human Exon: arome.affymetrix residuals Inf value
... Ah, thank you. ...
written 4 months 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 4 months ago by GENOMIC_region0 • updated 4 months ago by James W. MacDonald49k
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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 8 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 8 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 9 months ago by GENOMIC_region0

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