Volcano Plot Making

Question

[bikash2510]

How to make volcano plot from GSE data. I dont have p -value. and how to calculate p value from GSE data.

[Kevin Blighe]

Good evening, Please explain better what you want to do. No-one should want to create a volcano plot for no reason.

• Are you a beginner in bioinformatics?
• Is this a task or some assignment?
• On which dataset do you wish to focus?

Other threads by you:

• Volcano Plot Excel Sheet
• MATLAB Volcano Plot

[bikash2510]

GSE34747 Platforms (1)
GPL15069
Samples (6)

GSM854486 MSC_Ctrl_rep1 GSM854487 MSC_Ctrl_rep2 GSM854488 MSC_Ctrl_rep3 GSM854489 MSC_Li_rep1 GSM854490 MSC_Li_rep2 GSM854491 MSC_Li_rep3 I want to find out the differential gene expression bt VolcanoPlot of these samples.

[Kevin Blighe]

Thanks - there are some useful answers below. Please take a look and provide some feedback to tianleivv and Igor, if you wish.

Kevin

[Ram]

Do not add an answer unless you're answering your own principal question. If you're responding to someone, use Add Comment or Add Reply options. I'm moving your post to a comment now.

[bikash2510]

I a getting this error.

Your request could not be completed. Below is the R output which might give you a hint about possible errors. You may also consult documentation on GEO2R Limitations and caveats.

Loading required package: BiocGenerics Loading required package: methods Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

 clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
 clusterExport, clusterMap, parApply, parCapply, parLapply,
 parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

 IQR, mad, xtabs

The following objects are masked from 'package:base':

 Filter, Find, Map, Position, Reduce, anyDuplicated, append,
 as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
 eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
 lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
 pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
 tapply, union, unique, unlist, unsplit

Welcome to Bioconductor

 Vignettes contain introductory material; view with
 'browseVignettes()'. To cite Bioconductor, see
 'citation("Biobase")', and for packages 'citation("pkgname")'.

Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE)

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

 plotMA

ftp://ftp-ext.ncbi.nlm.nih.gov/geo/series/GSE34nnn/GSE34747/matrix/ Found 1 file(s) GSE34747_series_matrix.txt.gz trying URL 'ftp://ftp-ext.ncbi.nlm.nih.gov/geo/series/GSE34nnn/GSE34747/matrix/GSE34747_series_matrix.txt.gz' ftp data connection made, file length 656289 bytes ================================================== downloaded 640 KB

File stored at: /export/home/service/grid_nodes/geo2r_PROD/geo2r_JSID_01_568115_130.14.22.21_9000_geo2r_1520700578/GPL15069.soft Warning message: Partial NA coefficients for 2142 probe(s) Error in ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim, : No residual degrees of freedom in linear model fits Calls: eBayes -> ebayes Execution halted

[Ram]

bikash2510, please consider this your final warning. If you continue adding answers when you mean to add comments or replies to existing comments, your posts will be closed. If you have any questions on how to add comments or replies, ask me and I will point you to the resources.

[Ram]

I'm moving this answer to a comment.

Answer 1

[igor]

If you go to the GEO page for GSE34747, you'll see an "Analyze with GEO2R" button: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34747

GEO2R will allow you to analyze any microarray data in GEO right in the browser. You just have to specify which samples you want to compare. There is a nice tutorial here: https://biomedizin.unibas.ch/fileadmin/DKBW/redaktion/Group_Directories/Bioinformatics/IntroToRBioc/02_DEwithGeo2R_html.html

Answer 2

[tianleivv]

It depends on what kind of data you are using. For microarray data, I suggest limma package in R, and for RNA-Seq data I suggest DESeq2. Both of them can give you pvalues and fold changes for volcano plot.