User: minie

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minie0
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Posts by minie

<prev • 7 results • page 1 of 1 • next >
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RNA-Seq comparisons of various sample
... I want to analyze RNA-Seq with multiple samples with replicates. So I have two groups A & B and within that I have 5  different sub groups in each (a,b,c,d,e & a1,b1,c1,d1,e1).There are  two ways to perform the analysis : 1.A vs B 2.a_vs_a1 , b_vs_b1 ,c_vs_c1,d_vs_d1,e_vs_e1   which way wo ...
rna-seq written 5 days ago by minie0 • updated 5 days ago by Aaron Lun13k
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BS genome non-model organism
... I want to analyse RNA-Seq data for non-model organism using DESeq pacakge, organism is : Rhodnius proxilus http://metazoa.ensembl.org/Rhodnius_prolixus/Info/Annotation/#genebuild , I want to know  how shall I import this. ...
bsgenome written 21 days ago by minie0 • updated 19 days ago by Hervé Pagès ♦♦ 11k
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Comment: C: DESeq2 for R 3.1.3 version
... Hi Steve,   I tried that method but didn’t work , so its mentioned in the installation page of Bioconductor regarding different versions of installation. Kindly refer this page for 3.1 version of Rhttp://bioconductor.org/install/#install-bioconductor-packages ...
written 6 months ago by minie0
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DESeq2 for R 3.1.3 version
... Hello, i am trying to install DESeq2 for R 3.1.3, but it is throwing an error : package ‘DESeq2’ is not available (for R version 3.1.3) I know R is updated tp 3.3 and above , is there any way via which can install the libraries on R 3.1.3 version? Any help shall be much appreciated Thanks ...
bioconductor deseq2 R written 6 months ago by minie0 • updated 6 months ago by Steve Lianoglou12k
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Comment: C: Variance stabilizing transformation seems not working on NGS (bacterial 16srRNA
... Dear Wolfganag thanks for your reply, but with the limits also I am facing same problem : Error: Unknown parameters: limits Execution halted ...
written 6 months ago by minie0
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Answer: A: [DESEQ2] VST with rlog + normalization (size factor estimation) for downstream (
... Hello ! I am facing a problem while generating the plot , similar to what @John was doing.But the problem is I am getting an error with ylim i.e. Error: Unknown parameters: ylim Execution halted I dont know what is going wrong were. ...
written 6 months ago by minie0
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Answer: A: Variance stabilizing transformation seems not working on NGS (bacterial 16srRNA
... Hello!   I am facing some problem while running the same code. I am using following code: rld <- rlogTransformation(dds, blind=TRUE) vsd <- varianceStabilizingTransformation(dds, blind=TRUE) library("vsn") pdf(paste('plots/vsn_variance',expname,'.pdf',sep=''), height=4,width=12) par(mfrow= ...
written 6 months ago by minie0

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