down regulated and up regulated using r
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6 days ago

Is it possible to answer my question?

I am going to draw down-regulated and up-regulated using r or excel.

What parameter showed the RNA Seq samples are down regulated and up regulated ?

It is log2FoldChange values? or logFoldChange?

Thanks

analysis RNA Seq • 379 views
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How are you drawing down-regulated and up-regulated genes? Are you using a differential expression analysis tool like DESeq2 or edgeR? If yes, these tools usually output log2FoldChange values.

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I can not use DESeq2, because my data is not replicated. I am using R. I used basspase .illumina, but the graph is not clear. and it does not have pathway, and the graphs show down-regulated and up-regulated. But I have an excel file of the below parameters Gene Status log2(control Count) log2(comparison Count) Mean Count log2FC Std. Err. log2(Fold Change) q Value Significant.

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You can use the log2FoldChange values but why not include a heatmap on the pipeline?

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I am not sure if I add my data correctly because I see an error in my pipeline: eBayes(fit.cont) Error: evaluation nested too deeply: infinite recursion / options(expressions=)? Please read my comment I wrote in reply to " noahhelton98"

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6 days ago
noahhelton98 ▴ 10

I would definitely recommend analyzing your RNA-seq results in R, and as patelk26 said, those tools output Log2Foldchange values which is usually the standard when trying to determine differential expression of RNA-seq data. When you get the DESeq2 or edgeR results, it creates a dataframe (if you are following bioconductors pipeline for example) that you can easily filter in R for statistical significance and log2FoldChange using the dplyr package (here is a nice cheat sheet I use all the time https://www.rstudio.com/wp-content/uploads/2015/02/data-wrangling-cheatsheet.pdf ) .

I hope this helps, but if you could expand somewhat on your question and give some information on how you got to the step your at/what you have tried/where exactly you are trying to end up I am sure myself and others would be able to provide you with more help

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Thanks, I used the above link.

How can I add my data? my data is replaced with gse16873?

Is it possible to explain? I replace " mydata" with " gse16873". it says data set " mydata" not found

data(gse16873) cn=colnames(gse16873) hn=grep('HN',cn, ignore.case =T) adh=grep('ADH',cn, ignore.case =T) dcis=grep('DCIS',cn, ignore.case =T) print(hn)

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5 days ago

Is there any pipeline for no replate samples?

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