User: GENOMIC_region

Reputation:
0
Status:
New User
Last seen:
2 weeks, 5 days ago
Joined:
1 year, 8 months ago
Email:
s************@ymail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by GENOMIC_region

<prev • 18 results • page 1 of 2 • next >
0
votes
0
answers
60
views
0
answers
Comment: C: WGCNA: cleaning for sample outliers
... Hi Lluis,   Thank you very much. That helps. :) ...
written 19 days ago by GENOMIC_region0
1
vote
0
answers
60
views
0
answers
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 20 days ago by GENOMIC_region0 • updated 12 days ago by Bioconductor Community ♦♦ 0
0
votes
0
answers
60
views
0
answers
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 10 weeks ago by GENOMIC_region0
0
votes
1
answer
77
views
1
answers
Comment: C: Map exon level probeset to gene level probeset - Huex ST1.0
... Thank you very much. :) ...
written 10 weeks ago by GENOMIC_region0
2
votes
1
answer
77
views
1
answer
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 11 weeks ago by GENOMIC_region0 • updated 11 weeks ago by James W. MacDonald49k
0
votes
1
answer
95
views
1
answers
Comment: C: Human Exon: arome.affymetrix residuals Inf value
... Ah, thank you. ...
written 11 weeks ago by GENOMIC_region0
2
votes
1
answer
95
views
1
answer
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 11 weeks ago by GENOMIC_region0 • updated 11 weeks ago by James W. MacDonald49k
0
votes
1
answer
112
views
1
answers
Answer: A: comparing 2 long BED files in R in an efficient way
... Cross posted: https://www.biostars.org/p/324164/ ...
written 6 months ago by GENOMIC_region0
0
votes
0
answers
115
views
0
answers
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 6 months ago by GENOMIC_region0
0
votes
1
answer
232
views
1
answers
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 7 months ago by GENOMIC_region0

Latest awards to GENOMIC_region

Voter 11 weeks ago, voted more than 100 times.
Supporter 7 months ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 318 users visited in the last hour