Hello all,
I'm using the PCAplot function in cummerbund and I was wondering if anyone knows how to display the variance explained for...
19 results in 0.0023 seconds.
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CummeRbund PCAplot RNA-sequencing
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CummeRbund Expression Bar Plot
Hello,
I am running CummeRbund in R and I'm having an issue when it comes to the expressionBarPlot function.
I ran the... -
CummeRbund, extracting only one chromosome
So I'm new to R and want to create a scatterplot with cummeRbund that has only chr8 plots.
>pdf(file="practice_8.pdf")
...Last edited by ajsn6c; 06-21-2016, 04:43 PM. -
Modify cummeRbund plots in R studio: color, error bar width
Hello everyone,
I would like to reduce the horizontal length of the whiskers on the error bars on my expression plots, modify the color... -
cummeRbund error
Hello,
After completing all the analysis steps from Tophat to Cudiff, I am trying to plot the data using CummeRbund. But I get this error...Last edited by TPH; 01-21-2016, 12:37 PM. -
CummeRbund - PCA
Hello,
I'm using the PCA plot function implemented in the CummeRbund package. The package is very user-friendly, however, I can't find... -
PCA plot in cummeRbund with subset genes
Hello all,
I'm trying to create a PCA plot with my data. I managed to create it with all my genes using the standard script:
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csScatter: Error in match(x, table, nomatch = 0L)
hello everyone,
i am getting this error in csScatter command.
...Code:> csScatter(genes(cuff)) Error in match(x, table,
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NA entries in cummeRbund heatmap
Hi All,
I'm new to RNA-Seq and Bioinformatics. We have done a RNA-Seq study using Illumina Hi-Seq (paired-end, 90bp reads) on two cell... -
How to Filter Significant Genes??
Hi Everyone,
I am using cummeRbund to do some DE analysis and have 3 samples each having 5 biological replicates. Right now, the number... -
Gene ordered by ID using getGenes(), package CummeRbund
I want to produce a heat-map using a costumed gene list (accession IDs, e.g AT1G73590). I made a list of genes ordered depending on the processes they... -
Evaluating overdispersion in CummeRbund
Hi,
I am analyzing RNA-Seq data in a TopHat/Cufflinks/CummeRbund pipeline. In the CummeRbund manual, it is recommended that researchers check... -
Cuffdiff output shows log2(fold change) as infinite
Hi, I've compared two conditions in cuffdiff (2 reps each). On examining the output, I see in the gene_exp.diff file that some of the XLOC features show... -
Strange Dispersion and Density Plots in cummeRbund
Usually by the time I get to cummeRbund (having run TopHat, cufflinks, cuffmerge and cuffdiff) I see something in the dispersionPlot that looks at least... -
CummeRbund specify sample order, selecting specific chromosome
Hello community!
I have built a dataset of 30 individuals with varying phenotypes for whom I have complete transcriptome data for a specific...
