User: 786

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78650
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Posts by 786

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Comment: C: Secondary structure prediction correctness meassure
... Hi I want to predict the secondary structure of amino acids of protein by retrieving it from PDB in R. How can I use PredictHEC? What could be the raw code for this purpose? ...
written 4 weeks ago by 78650
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GENEMANIA: Single gene query
... Hi I'm working on Gene-Gene interaction through GENEMANIA tool. I want to search only one gene as query but whenever I entered it in search I got error. I just wanted to ask that can't we use single gene as query in it? and plz let me know some other tools which can be used to find out gene-gene int ...
gene genemania written 21 months ago by 78650 • updated 21 months ago by Jean-Karim Heriche19k
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Comment: C: Comparison of Affymetrix with other platforms
... Thank u for your concern. What would be the reasons for bioinformatics based research? ...
written 2.4 years ago by 78650
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Comparison of Affymetrix with other platforms
... Hi, I want to ask that most of the microarray data-based studies are conducted by using **Affymetrix** data. Although there are many other platforms on which microarray analysis is being carried out then why Affymetrix is preferred in most of the studies. Is there any reason for this biasness? ...
geo illumina bioconductor rna-seq affymetric written 2.4 years ago by 78650
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GEO and CDF files
... Hi, I need a help from your side. I need microarray data for a project. I have two options available for this task. One is to use disease related studies from GEO and then apply R to extract genes associated with the disease of interest that I want to work on. Second option is to use custom CDF fil ...
geo microarray affymetrix written 2.4 years ago by 78650
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GEO studies included very few subjects having extreme statistical power
... Hi everyone! I couldn't understand this I need your help that why some GEO studies included very few subjects and however have an extreme statistical power (a lot of genes significant)?? Please help me in understanding this. ...
geo R gene written 2.7 years ago by 78650 • updated 2.7 years ago by 12021560-00210
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Comment: C: Error in fit2 commands
... I think it is present in following commands fit2 = contrasts.fit(fit, cont.matrix) fit2 = eBayes(fit2) ...
written 2.9 years ago by 78650
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Error in fit2 commands
... Hi everyone I was working on R and want to retrieve differentially expressed genes but got an error in the fit2 commands. I'l be very thankful if anyone can help me in removing it. study3 = "GSE22309" gse22309dat = getGEO('GSE22309') gse22309raw= getGEOSuppFiles(study3) tar ...
annotate R bioconductor affy limma written 2.9 years ago by 78650 • updated 2.9 years ago by Mike1.3k
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Comment: C: Unreliable results of R while retrieving DEG
... groups = pData(phenoData(gse55650dat[[1]]))$source_name_ch1 groups=as.character(groups) groups[groups=="Control myoblasts"]="non.diabetic" groups[groups=="Diabetes myoblasts"]="diabetic" groups[groups=="Control myotubes"]="non.diabetic" groups[groups=="Diabetes myotubes"] ...
written 3.0 years ago by 78650
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Unreliable results of R while retrieving DEG
... Hi I was working on GSE55650 and received different number of differentially expressed genes just by changing the group format. Although the control and diseased were same in both types of groups but still get different number of genes. I just don't understand why is it so?Can anyone help me in unde ...
R geoquery affy limma written 3.0 years ago by 78650

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Popular Question 29 days ago, created a question with more than 1,000 views. For Allele Frequency Calculator
Popular Question 29 days ago, created a question with more than 1,000 views. For Error in design matrix command of R
Popular Question 29 days ago, created a question with more than 1,000 views. For Error in R Script
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Allele Frequency Calculator
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Error in design matrix command of R
Popular Question 21 months ago, created a question with more than 1,000 views. For Allele Frequency Calculator
Popular Question 21 months ago, created a question with more than 1,000 views. For Error in design matrix command of R
Popular Question 21 months ago, created a question with more than 1,000 views. For Error in R Script
Popular Question 21 months ago, created a question with more than 1,000 views. For PLINK and 1000 Genome browser
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