User: gokce.ouz

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gokce.ouz60
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Posts by gokce.ouz

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Comment: C: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
... I really appreciate for your detailed answer Valerie. ...
written 2.8 years ago by gokce.ouz60
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Comment: C: WGCNA - How to prevent "blockwiseModules" command from dividing genes into multi
... Thank you for your answer Peter. While importing results from WGCNA to external network programs I found it difficult to using multiple TOM (still newbie at the field) . Even though different blocks genes has zero TOM https://support.bioconductor.org/p/70092/, I wanted to analyse using single block ...
written 2.8 years ago by gokce.ouz60
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Comment: C: WGCNA - How to prevent "blockwiseModules" command from dividing genes into multi
... Hi Marge, In our server/ cluster, users have limited time (24 hours) to actively use R in interactive queue. That is why I wrote "it never finishes". In other words it is my connection problem nothing related to the program. The max 46K genes explained below by Dr. Peter Langfelder, it is the numb ...
written 2.8 years ago by gokce.ouz60
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WGCNA - How to prevent "blockwiseModules" command from dividing genes into multiple blocks?
... Hi,  I am using RNA-Seq data for WGCNA. I have 34 samples. For my WGCNA analysis, I am using o networkType=Signed hybrid, TOM=Signed, corType=bicor, pearsonFallback = "individual" & deepSplit= 2 . nethybrid.2 = blockwiseModules(datExpr, power = softpower,maxBlockSize = 46000, ...
wgcna rna-seq written 2.8 years ago by gokce.ouz60 • updated 2.8 years ago by Peter Langfelder2.1k
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Comment: C: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
... Thanks a lot for the suggestion and clarification Johannes. I will implement it to my analysis as soon as I solve my R version  problem. Actually when I was running the code with org.Hs.eg.db, I was expecting to see all the corresponding HGNC symbols but it did not return which actually surprised m ...
written 2.8 years ago by gokce.ouz60
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Comment: C: Pre-processing of RNA-Seq data for WGCNA and DGE
... I really appreciate your help. Thanks a lot! Best Regards, Gokce ...
written 2.8 years ago by gokce.ouz60
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How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
... Hi, I am analysing my RNA-Seq data with DESeq2. At the end I would like to convert significantly expressed  ensembl IDs to GeneSymbols. I am using AnnotationDbi for this. However, I realized that not all the ensembl IDs are converted to Gene Symbols. 25072 out of 48607 returned as NA. More than 110 ...
rnaseq annotationdbi written 2.8 years ago by gokce.ouz60 • updated 2.8 years ago by Valerie Obenchain6.7k
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Comment: C: Pre-processing of RNA-Seq data for WGCNA and DGE
... Many many thanks Peter, your answers relieved me a lot. I will also run without setting the batch as covariate. One last question : How can I understand which run gives me the most accurate results ? For example, when I increase the maxBlocksize parameter from 10.000 to 20.000, naturally  all the m ...
written 2.8 years ago by gokce.ouz60
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Comment: C: Pre-processing of RNA-Seq data for WGCNA and DGE
... Thanks a lot for your answer Peter. As you mentioned I have two distinct group but 1 disease patient (Sph4)  is clustering together with control patients at the right- cluster, so I thought it as outlier. But, you suggest me not to remove it, right ? For my WGCNA analysis, I am using networkType=Si ...
written 2.8 years ago by gokce.ouz60
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Comment: C: Pre-processing of RNA-Seq data for WGCNA and DGE
... Hi Michael,  I guess I explained myself wrong.  As you said, I am using the DESeq() on raw counts then using results() on the "dds" variable to do DGE with defining the contrasts & alpha. The aim of rld or vsd transformation is for EDA and to see how samples are clustering via PCA, hierarchical ...
written 2.8 years ago by gokce.ouz60

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