User: sbbinfo90

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sbbinfo900
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Posts by sbbinfo90

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Comment: C: Vidger library error
... [39] annotate_1.59.1             IRanges_2.15.17             [41] ggplot2_3.0.0               SummarizedExperiment_1.11.6 [43] nnet_7.3-12                 BiocGenerics_0.27.1         [45] lazyeval_0.2.1              survival_2.42-6             [47] magrittr_1.5                crayon_1.3.4        ...
written 7 months ago by sbbinfo900
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Comment: C: Vidger library error
... loaded via a namespace (and not attached):  [1] Biobase_2.41.2              tidyr_0.8.1                  [3] edgeR_3.23.3                bit64_0.9-7                  [5] splines_3.5.1               Formula_1.2-3                [7] assertthat_0.2.0            stats4_3.5.1                 [9] lat ...
written 7 months ago by sbbinfo900
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Comment: C: Vidger library error
... Sure, > sessionInfo() R version 3.5.1 (2018-07-02) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS: /home/sbharti/Softwares/R_351/lib64/R/lib/libRblas.so LAPACK: /home/sbharti/Softwares/R_351/lib64/R/lib/libRlapack.so locale:  [1] ...
written 7 months ago by sbbinfo900
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Comment: C: WGCNA Co-expression network analysis on cuffdiff output
... Hello Peter, I have 8 samples (1 control and 7 infection stages) and my objective is to study genes co-expression amongst all pairwise comparisons. I already have Differentially expressed genes from Cuffdiff for all comparisons also. Can you please guide how to perform WGCNA on such data?   There ...
written 7 months ago by sbbinfo900
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Comment: C: How to get an output from DESeq2 to be used in WGCNA package
... Hi Peter, Can you please send link for this tutorial https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/faq.html as it is not available now? ...
written 7 months ago by sbbinfo900
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WGCNA Co-expression network analysis on cuffdiff output
... Hello, I am struggling with running WGCNA on cuffdiff output consisting of 28 pairwise comparisons (Time series Analysis). Can someone suggest way out to perform WGCNA for each comparisons separately? Thanks! ...
wgcna cuffdiff written 7 months ago by sbbinfo900
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Comment: C: Error:object 'lookup_tax_id_by_organism' not found with makeOrgPackageFromNCBI
... Hello James, Can you comment on this thread https://support.bioconductor.org/p/113034/ ? ...
written 7 months ago by sbbinfo900
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Vidger library error
... Hello, I am using VIDGER from bioconductor but it shows an error: vsMAMatrix(data = cuffdiffdata, d.factor = NULL, type='cuffdiff',padj = 0.05, y.lim = NULL, lfc = NULL, title = TRUE, legend = TRUE,grid = TRUE, counts = TRUError in `$<-.data.frame`(`*tmp*`, "id_x", value = "24hpi") :   replace ...
vidger written 7 months ago by sbbinfo900
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Comment: C: [maSigPro] two color array analysis of time series in different cell lines.???
... $groups.vector  [1] "X12hours_post_infectionvsControl" "X24hours_post_infectionvsControl"  [3] "X2days_post_infectionvsControl"   "X4days_post_infectionvsControl"    [5] "X6days_post_infectionvsControl"   "X8days_post_infectionvsControl"                          ......[63] ...
written 7 months ago by sbbinfo900
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Comment: C: [maSigPro] two color array analysis of time series in different cell lines.???
... $edesign    Time Replicate Control X12hours_post_infection X24hours_post_infection X2days_post_infection 1     0         1       1                       0                       0                     0 2     0         2       1                       0                       0                     0 3   ...
written 7 months ago by sbbinfo900

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