User: iside

gravatar for iside
iside10
Reputation:
10
Status:
New User
Location:
European Union
Last seen:
4 months, 3 weeks ago
Joined:
4 years, 6 months ago
Email:
m*************@gmail.com

Posts by iside

<prev • 12 results • page 1 of 2 • next >
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Magma gene-based analysis
... Hi all, I have used MAGMA as implemented in FUMA to run a gene-based analysis, using GWAS summary statistics. I now have a certain number of significant genes, in different regions compared to the ones that were significant in the GWAS. I looked at MAGMA paper and it seems it used mean or top statis ...
gwas gene-based analysis fuma magma written 5 months ago by iside10
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Ensembl Biomart Allele Frequency for different ethnicity
... Hi all, I am using Ensembl BioMart to retrieve the allele frequency for a list of SNPs. I need to have this information for different ethnicities, but I cannot find any appropriate filter. I know this is possible on the Ensembl main web site, but I would need to do it one SNP at the time and I woul ...
maf allele frequency snps ensembl biomart written 11 months ago by iside10
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Comment: C: Can I normalize my data twice?
... Hi Ron, thanks for your comment! Actually the values are not between 0 and 1 but between -3 and +3, I am not sure how the normalization has been done exactly as I got this file as it is... ...
written 3.0 years ago by iside10
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Can I normalize my data twice?
... Dear all, I am working on a dataset containing 700 samples and 50000 genes, which has been rank normalized. For my purposes, I calculated the Pearson's residuals of each gene including covariates and technical confounders is the model. The data I produced has not a normal distribution though. Bea ...
normalization normal distribution data analysis written 3.0 years ago by iside10
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Comment: C: Limma analysis - decomposition problem
... I get only a matrix of NAs! ...
written 4.2 years ago by iside10
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Comment: C: Limma analysis - decomposition problem
... I have only 2 conditions. Either case or control.  ...
written 4.2 years ago by iside10
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Comment: C: Limma analysis - decomposition problem
... Hi Andrew, thanks for your reply.  The data had already been normalised, and corrected for batch effect with the package Combat. The output you asked for is the following: range(expression) [1]  6.109361 16.553681. My design matrix is composed by two columns: Intercept (136 rows set to 1) and   ...
written 4.2 years ago by iside10
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Limma analysis - decomposition problem
... Dear all, I am running a differential expression analysis with limma. My dataset includes unrelated individuals as well as twins, and I am aware that limma is not designed to deal with familiar data, but, as explained in the users' guide I may use the family as a blocking variable (in this way limm ...
lmfit cholesky limma duplicatecorrelation written 4.2 years ago by iside10 • updated 4.2 years ago by andrew.j.skelton735.8k
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Sva batch correction for rna seq
... Dear all, I am performing a differential expression analysis with deseq2, but I have firstly to take into account batch effects.  I have an info file with several technical confounders and other information for the samples (twins), like family and zygosity. As you suggested, I am using the svaseq f ...
sva deseq2 rna-seq batch-correction written 4.3 years ago by iside10 • updated 4.2 years ago by Biostar ♦♦ 20
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Comment: C: RNA-seq counts analysis with DESeq
... Yes, it seems what I need! I will try with SVA, thank you.  ...
written 4.3 years ago by iside10

Latest awards to iside

Popular Question 2.8 years ago, created a question with more than 1,000 views. For Limma analysis - decomposition problem
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Sva batch correction for rna seq
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Can I normalize my data twice?
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Sva batch correction for rna seq

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