User: krushnach80

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krushnach80320
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Posts by krushnach80

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Comment: C: WGCNA pearson or bicor? Also, should I adjust module correlation Pvalues by Bonf
... the object formed is logical , its a R question plus bit of simple maths why not go for std dev instead of variance ? like can i consider genes that falls within my first two Std deviation ? i would be glad if you can bit explain more when i see the object `keep` its says logical , how do you su ...
written 2 days ago by krushnach80320
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Comment: C: Problem for getting P-Value in Module-Trait Relationship in WGCNA
... will use this enhanced version ...
written 2 days ago by krushnach80320
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Comment: C: Using Circos plot to visualize RNA-seq data
... @badredda if you considering volcano plot then this is an elegant way to show [volcano plot][1] [1]: https://www.biostars.org/p/309962/#324664 ...
written 25 days ago by krushnach80320
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Comment: C: Using Circos plot to visualize RNA-seq data
... have you seen the circos manual they have some proper documentation ...you have to make your datafiles as such given in the tutorial with chromosome number [circos][1] [1]: http://circos.ca/tutorials/lessons/configuration/data_files/ ...
written 25 days ago by krushnach80320
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Comment: C: GSEA output interpretation
... as you can see the figure..where i see the red portion vs blue portion...so since in this comparison i have HSC vs LSC where HSC is my control and LSC my test..so can you tell me what i read is the red one show high enrichment ,the can i tell that the genes that are in the red portion are enriched a ...
written 27 days ago by krushnach80320
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Comment: C: General questions about running GSEAPreranked
... https://github.com/samuelwb/cancer-evolution/blob/master/RnaSeqSignaturesSsGsea/ssGSEA.r ...
written 29 days ago by krushnach80320
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GSEA output interpretation
... I have done the diffrential gene expression for stages , i did the GSEA for the same as one of my comparison i had made is Normal Stem cell vs leukemic stem cells ,so i have few doubts ,one of them is about the core enrichment which i see in the excel output ..what does that mean when it says "YES" ...
gene rna-seq written 4 weeks ago by krushnach80320 • updated 28 days ago by h.mon18k
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Comment: C: Resources for gene signature creation
... not fully but im moving at a snail's pace....i updated my doubt ...
written 4 weeks ago by krushnach80320
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Comment: C: Resources for gene signature creation
... okay..now it helped me to get a hang of it i was seeing the code but unable to figure it out let me try and let you know and this is the first error i encounter actually im using your code which you made [regression][1] so the model is listModels not sure if im doing it correct or not Error ...
written 4 weeks ago by krushnach80320
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Comment: C: Resources for gene signature creation
... naive question what is "Mymodel" is it the input matrix ? ...
written 4 weeks ago by krushnach80320

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