User: seta

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seta1.3k
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Posts by seta

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Microarray data normalization
... Dear all, Sorry for such a basic question, but I got confused. As far as I know, the RMA method implemented in affy package is a standard method for microarray data normalization. Could you let me know if the main code `data.rma.norm = rma(raw.data)` normalize data in three stages, background corre ...
normalization rma microarray written 4 days ago by seta1.3k • updated 4 days ago by Kevin Blighe63k
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Comment: C: GWAS analysis using linear mixed model
... Any suggestions! please ...
written 27 days ago by seta1.3k
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Linear mixed model and GWAS analysis
... Dear all, I would like to test the possible association of a set of SNPs located on a given gene with a quantitative trait that measured at the several time point (every two years) during a longitudinal cohort study. As far as I know, the linear mixed model can be used for this analysis, I'm lookin ...
gwas longitudinal linear mixed model cohort written 29 days ago by seta1.3k
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Comment: C: Phenotype from plink fam file in gcta
... Hi Kevin, In the case of a longitudinal cohort study, the SNP association analysis can be done by the linear mixed model as implemented in MLMA, yes? Could you please tell me how to put all measurements of a given variable (trait) at each time point in the "test.phen" file? Many thanks ...
written 4 weeks ago by seta1.3k
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Physical interaction of long non-coding RNAs with target genes
... Dear all, As we know, some long non-coding RNAs (lncRNAs) have the trans-regulatory role via the physical interaction with target genes. Assuming these lncRNAs or their corresponding target genes or both of them (lncRNA and target gene) were down-regulated. At these conditions, can we say the effec ...
target genes physical interaction lncrna written 5 weeks ago by seta1.3k
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Comment: C: Validation of protein-coding gene and lncRNA correlation
... Thanks. As far as I know, this package also works based on the correlation. Any other suggestions? ...
written 8 weeks ago by seta1.3k
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Validation of protein-coding gene and lncRNA correlation
... Dear all, I obtained several correlations (based on Spearman test) between some differentially expressed protein-coding genes and long non-coding RNA (lncRNAs) obtained from a RNA-seq analysis (human). However, I would like to further validate these observed correlations using in silico analysis, n ...
correlation rna-seq non-coding rna lncrna written 9 weeks ago by seta1.3k • updated 8 weeks ago by caggtaagtat1.1k
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Classification of long non-coding RNAs
... Dear all, As far as I know, the long non-coding RNAs can be classified into different categories (sense, antisense, intronic, intergenic, bidirectional) based on their location with respect to protein-coding genes. Could you please let me know how I can obtain such information for human long non-c ...
non-coding rna lncrna written 11 weeks ago by seta1.3k • updated 11 weeks ago by genomax87k
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Comment: C: long-non coding RNA and protein-coding genes correlation
... Hi Carlo, Thanks for your explanation. Splitting ncRNA into different categories is a good idea, I also saw the ncRNA classification into 5 categories (intergenic, antisense, intronic, bidirectional, enhancer RNA). Could you let me know how I can annotate my lncRNA as the corresponding categories? ...
written 12 weeks ago by seta1.3k
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long-non coding RNA and protein-coding genes correlation
... Dear all, I have got some differentially expressed (DE) lncRNA and DE coding genes from an RNA-seq analysis (human). Then, I did a co-expression analysis to get the co-expressed DE coding genes with DE lncRNA. As the RNA-seq data (CPM was used) was not normal, I used the Spearman correlation test. ...
co-expression correlation rna-seq lncrna written 12 weeks ago by seta1.3k • updated 12 weeks ago by Carlo Yague5.0k

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