User: modarzi

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modarzi130
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Posts by modarzi

<prev • 157 results • page 1 of 16 • next >
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Comment: C: How can I annotate microarray data set through Ensemble Id?
... Dear Dr. Blighe Thanks for your comment. I also, add `'ENTREZID'` in your code. but as you see for `1007_s_at` I have 8 'Ensemble Id'. Their Gene Symbol is DDR1 and MIR4640. So, exactly my question is which 'Ensemble Id' should I use for `1007_s_at` at DDR1? or by which mechanism I can understand ...
written 10 weeks ago by modarzi130
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How can I annotate microarray data set through Ensemble Id?
... Hi, I am studying on microarray data set which its platform is the GPL 96([HG-U133A] ). Consequently, I used the GPL 96 annotation file to annotate gene expression data and convert probe ids into gene identifiers. My problem is that in the annotation file I see three columns as gene identifiers inc ...
ensemble id gpl 96 affymetrix written 10 weeks ago by modarzi130 • updated 10 weeks ago by Kevin Blighe65k
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Comment: C: how does find the normalization method in GSE in GEO for microarray data?
... Dear Friederike Really thanks for your comment. But, I would like to know the output of Affymetrix GeneChip analysis software MAS 5.0 is normal or not? and if yes, by which method, microarray data has been normalized? As you know, few methods such as RMA has been published for microarray normalizin ...
written 10 weeks ago by modarzi130
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Comment: C: how does find the normalization method in GSE in GEO for microarray data?
... Dear Friederike Thanks for your comment. In fact, I don't know Affymetrix GeneChip analysis software MAS 5.0 and its output. This is my question that how can I find method of normalization in GSE2034? I appreciate it if you share your comment with me. Best Regards, ...
written 10 weeks ago by modarzi130
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how does find the normalization method in GSE in GEO for microarray data?
... Hi, I would like to use microarray data from GSE2034 but I can't find the method of normalization of that. So, I downloaded the paper of that data (Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer). In gene expression analysis section of that paper ...
normalization mas 5.0 method microarray written 10 weeks ago by modarzi130
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finding AUC and AUCPR in gene regulatory network through ARACNE and CLR methods
... Hi, I reconstruct gene regulatory network through ARACNE and CLR methods for 2 datasets(main and gold standard datasets). Now, I would like to Calculate AUC(Area Under the Curve) and AUCPR(area under the precision-recall curve) for that two methods. Since I use R platform and Cytoscape for my an ...
grn auc ckr aucpr aracne written 12 weeks ago by modarzi130
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Comment: C: How to compare 2 separate coexpression networks each with the same genes?
... Dear Dr. Hériché I need your comment. I would like to compare two co-expression network belong two different cancers, Lung and Breast. can I map your propose approach(Tensor factorizations for dynamic graphs) to my research target? I appreciate if you share your comment with me. Best Regards, ...
written 3 months ago by modarzi130
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Comment: C: Problem relate to running ClueGO in Cytoscape
... Hi, I upgrade my Cytoscape and that problem was solved. Thanks ...
written 3 months ago by modarzi130
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Problem relate to running ClueGO in Cytoscape
... Hi, For Gene enrichment analysis, I used ClueGO as a Cytoscape plugin. At first, I updated ontologies.then, to enrichment analysis for my 40 Ensemble ids, I executed ClueGO in Cytoscape. The process will be continued but in the final stage for getting the GO network, my Cytoscape is closed suddenly ...
cluego cluepedia cytoscape written 5 months ago by modarzi130 • updated 4 months ago by scooter360
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Comment: C: Problem for Running "multivariate Cox proportional hazards model"
... Ok, You mean that I should consider "LogRank", "HR", "HRlower" , and "HRupper" for ranking my genes. but how can I take into account them at the same time for ranking task? Best Regards, ...
written 5 months ago by modarzi130

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Popular Question 12 weeks ago, created a question with more than 1,000 views. For how to calculate or extract Circular RNA expression via RNA-seq data
Popular Question 5 months ago, created a question with more than 1,000 views. For problem for constructing Topological Overlap Matrix (TOM) in WGCNA Algorithm
Popular Question 7 months ago, created a question with more than 1,000 views. For Evaluation of HISAT2 Alignment Result
Popular Question 7 months ago, created a question with more than 1,000 views. For data pre-processing for WGCNA Algorithm
Popular Question 9 months ago, created a question with more than 1,000 views. For problem for constructing Topological Overlap Matrix (TOM) in WGCNA Algorithm
Student 10 months ago, asked a question with at least 3 up-votes. For Problem for getting P-Value in Module-Trait Relationship in WGCNA
Popular Question 10 months ago, created a question with more than 1,000 views. For problem for constructing Topological Overlap Matrix (TOM) in WGCNA Algorithm
Popular Question 12 months ago, created a question with more than 1,000 views. For Error for reading .gtf file in R
Popular Question 12 months ago, created a question with more than 1,000 views. For Evaluation of HISAT2 Alignment Result
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Popular Question 14 months ago, created a question with more than 1,000 views. For Evaluation of HISAT2 Alignment Result
Student 14 months ago, asked a question with at least 3 up-votes. For Problem for getting P-Value in Module-Trait Relationship in WGCNA
Popular Question 15 months ago, created a question with more than 1,000 views. For how to calculate or extract Circular RNA expression via RNA-seq data
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Popular Question 15 months ago, created a question with more than 1,000 views. For Evaluation of HISAT2 Alignment Result
Popular Question 19 months ago, created a question with more than 1,000 views. For how to calculate or extract Circular RNA expression via RNA-seq data
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