User: iphoenix2100

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iphoenix210040
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Location:
European Union
Last seen:
5 years, 2 months ago
Joined:
5 years, 9 months ago
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Posts by iphoenix2100

<prev • 19 results • page 1 of 2 • next >
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Chromatin state segmentation - direction of effect of the identified enhancer
... Dear all, I am using this UCSC genome browser to do some functional annotation on the top SNP and its high LD SNPs. And would like to know the chromatin state segmentation. My top SNP is located in the intergenic region of GENE1 and GENE2. From the UCSC chromatin data is seems like both these gene ...
chip-seq sequencing written 5.2 years ago by iphoenix210040 • updated 5.2 years ago by Ryan Dale4.9k
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Comment: C: z score transformation from signal intensities of raw microarray data
... Thanks Mr. Singh,, It seems the data in repository is all normalized microarray expression values or that is what the readme file of the data says .. what options do I have in that case - can I calculate the zscore by the methods that i have mentioned in my query or not! thanks again for your sugg ...
written 5.3 years ago by iphoenix210040
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z score transformation from signal intensities of raw microarray data
... DEar all, I am making this slow transition from GWAS findings to expression datasets. We are using an online repository of microarray data from different donors (arrayed for different regions of the brain). And basically we are using a set of genes from the initial GWAS findings and see how it is a ...
microarray written 5.3 years ago by iphoenix210040 • updated 5.3 years ago by Manvendra Singh2.1k
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genomic inflation/deflation -- correction using Robust options
... Dear all, I am running a Gene X environment interaction analysis, where I am testing if the interaction of the phenotype with an environmental variables that shows any significant association. For this I am implementing the Robust Standard error option implemented in probabel ---- that actually ac ...
gwas sequencing written 5.3 years ago by iphoenix210040 • updated 5.2 years ago by Biostar ♦♦ 20
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Comment: C: Can Y chromosome be imputed?
... Thanks for the comment... so you mean 24 in this case,,,,... I think there is some option for such imputation in PLINK... But how accurate they are (heard from a recent conference of to use superior prog/ or dedicated prog. such as IMPUTE2.) Any ideas. Thanks in advance ...
written 5.4 years ago by iphoenix210040
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Can Y chromosome be imputed?
... Dear all, I am new to imputation and just got to know the imputation method for autosomes using MINIMAC (SHAPEit).... There seems to be an option in minimac to impute the x Chromosome... but could not find any reference pertaining to Y chromosome. Which makes me wonder can Y be imputed - if so wha ...
gwas sequencing written 5.4 years ago by iphoenix210040 • updated 5.4 years ago by gaurav.singh10
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test statstic used in probabel for GWAS
... Dear All, I am new to genetic analysis (GWAS). What is the test statistic used in Probable for main-effects analysis. (asymptotic distribution, X2 or t-distribution), Thanks for the clarifications.     ...
gwas probabel sequencing written 5.4 years ago by iphoenix210040
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plotting SEs against allele frequency in R
... Dear all,  I have a dataset with two Standard errors from different experiments of *GWAS. And trying to see how it varies against the allele frequency. This to discard any outliers from the following analysis. so the dataset looks like $maf $SE1 $SE2 0.01  0.356  0.348 0.05  0.456  0.245 ..... ...
R written 5.5 years ago by iphoenix210040 • updated 5.5 years ago by Biostar ♦♦ 20
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BETA(direction of effect) sign flipping based on the coded allele - when doing meta analysis of different studies - explain?
... Hi all,     So I am doing this new analysis (meta) from different studies. In which I was asked - to swap the coded and non-coded alleles - and the direction/sign of the beta flipped to make both consistent across studies. I am not able to understand this part or the reason why it is being do ...
gwas meta snp written 5.6 years ago by iphoenix210040 • updated 5.6 years ago by David W4.7k
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Assigning locus to set of SNPs based on its chromosome position
... Hi all,     So I have this tab-delim file with information on (following columns) SNP    CHR    POS   Allele1    Allele2    A.Freq1    Effect    StdErr    P.value - Now I would like to assign the SNPs to its corresponding locus based on the chromosome position.  As I am new in this field - i f ...
genome assembly written 5.6 years ago by iphoenix210040 • updated 5.6 years ago by Bert Overduin3.7k

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