User: Sib

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Sib20
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Posts by Sib

<prev • 38 results • page 2 of 4 • next >
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Comment: C: Error in volcano plot drawing with R.
... In fit object, there are no p-values ...
written 9 weeks ago by Sib20
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Comment: C: Error in volcano plot drawing with R.
... I am new to this analysis and I don't know whether It should have p-value or not But when I call fit, the results are these: > fit An object of class "MArrayLM" $coefficients Normal Tumor A_19_P00315452 7.134198 6.256601 A_19_P00315459 6.925040 7.04657 ...
written 9 weeks ago by Sib20
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Error in volcano plot drawing with R.
... I want to draw a volcano plot. I don't know where I make a mistake that I get an error. These are the codes: library(Biobase) library(GEOquery) library(ggplot2) library(pheatmap) library(limma) library(plyr) gset<-getGEO("GSE116959",GSEMatrix = TRUE,AnnotGPL = TRUE,de ...
R written 9 weeks ago by Sib20 • updated 9 weeks ago by serovop5410
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Comment: C: After differential expression analysis if we use gene symbols for further analys
... It is an identifier. I think its complete name is HGNC-GENE-SYMBOl. ...
written 9 weeks ago by Sib20
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Comment: C: String db knows some gene symbols of DEGs for more than one protein and after e
... thanks to reply my question. I also have tried ensemble IDs. But the same problem occurs is about ensemble IDs. I saw in many related articles researchers used GENE-SYMBOLs for transferring genes from GEO to STRING and I was wondering about that because they lose many DEGs. ...
written 9 weeks ago by Sib20
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Comment: C: After differential expression analysis if we use gene symbols for further analys
... thank you for answering. Sorry, I think I explained badly. My meaning of DEG symbols was GEN_SYMBOLs of DEGs. In other words I have a list of DEGs in GENE_SYMBOl format. ...
written 9 weeks ago by Sib20
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Comment: C: Expression correlation tool
... The file is destroyed. would you please introduce another good tutorial? ...
written 9 weeks ago by Sib20
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Differentially expressed genes visualization with Cytoscape
... I performed a differential expression analysis and I have a list of DE human genes. now, I want to visualize DEGs by Cytoscape (showing up-regulated and down-regulated proteins with different shapes and set the size of the nods on the base of levels of expression.) but this work needs a network and ...
ppi network visualization cytoscape written 10 weeks ago by Sib20 • updated 10 weeks ago by padwalmk80
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String db knows some gene symbols of DEGs for more than one protein and after entering gene symbols ask to select the desiered gene.
... I performed a differential expression analysis with R. Now I have a list of differential expressed gene symbols and I want to visualize them with Cytoscape. When I enter DE gene symbols to sring db plugin of Cytoscape, it knows some of the gene symbols for more than one protein and asks to choose be ...
R string app cytoscape network visualization written 10 weeks ago by Sib20 • updated 10 weeks ago by scooter140
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After differential expression analysis if we use gene symbols for further analysis we lose some DEGs. Is it ok?
... I performed a differential expression analysis by R. Now, I have a list of DEG GENE-SYMBOLs. My problem is that not all the DEGs had gene symbols. I am worried to lose some of the data by using gene symbols. But I see many articles used gene symbols. Is it a routine thing and we can not do something ...
geo differential expression analysis written 10 weeks ago by Sib20

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