User: rkp

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rkp0
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Posts by rkp

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Comment: A: How to extract common genes that are DE in each comparisons?
... > is.de <- decideTests(fit2, method="global") > de.in.all <- rowSums(is.de!=0) == ncol(is.de) > length(de.in.all) [1] 22810 > up.in.all <- rowSums(is.de == 1) == ncol(is.de) > length(up.in.all) [1] 22810 ...
written 4 months ago by rkp0
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Comment: A: How to extract common genes that are DE in each comparisons?
... Hi Aaron, Thank you very much for your reply but I am unable to find genes that are DE in all comparisons. It given the probe id of all the genes present in datasets instead of DEG. > is.de <- decideTests(fit2, method="global") > de.in.all <- rowSums(is.de!=0) == ncol (is.de) > leng ...
written 4 months ago by rkp0
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How to extract common genes that are DE in each comparisons?
...  I have made a Contrasts matrix as  design <- model.matrix(~0+f) colnames(design) <- levels(f) design fit <- lmFit(eset,design) names(fit) cont.matrix <- makeContrasts(C9T9="Control9-Treated9",C24T24="Control24-Treated24",........................................,levels=design) cont.matr ...
limma R bioconductor affymetrix microarrays written 4 months ago by rkp0
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Heatmap error: 'ColSideColors' must be a character vector of length ncol(x)
... > library("gplots") > heatmap.2(exprs(esetSel), col=topo.colors(75), scale="none", ColSideColors=patientcolors, +           key=TRUE, symkey=FALSE, density.info="none", trace="none", cexRow=0.5) Error in heatmap.2(exprs(esetSel), col = topo.colors(75), scale = "none",  :    'ColSideColors' mus ...
microarray limma bioconductor written 4 months ago by rkp0 • updated 4 months ago by Gordon Smyth30k
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Comment: C: R script for getting Common DEG genes from all comparisons by limma analysis
... Dear Gordon, Thank you very much for providing script but I have not found DEG for all contrast. It is showing NULL > results <- decideTests(fit2) > i <- rowSums(results != 0) == ncol(fit2) > fit2$genes[i,] NULL   ...
written 4 months ago by rkp0
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R script for getting Common DEG genes from all comparisons by limma analysis
... Dear All, I want to find the probe id of Common genes that are differentially expressed between all the comparisons by limma analysis. Any suggestions will be greatly appreciated. With kind regards, Rajesh ...
microarray limma R bioconductor written 4 months ago by rkp0 • updated 4 months ago by Gordon Smyth30k
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R script for construction of VennDiagram for eight sample
... Hi all, I wish to construct VennDiagram for eight sample comparison in limma analysis. Any suggestions will be greatly appreciated. Thanks.  Rajesh ...
limma R bioconductor written 4 months ago by rkp0 • updated 4 months ago by Aaron Lun14k
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What are the expression value of genes/probes in limma results of topTable
... Dear All, Kindly suggest me which value are expression value in the following table that can be utilized for plotting Heatmap.      logFC   AveExpr         t      P.Value    adj.P.Val        B   -6.828181  7.966478 -18.82087 5.665531e-14 5.032385e-10 21.33399   4.855277 10.119313  18.69994 6.38444 ...
heatmap written 12 months ago by rkp0 • updated 12 months ago by Aaron Lun14k
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Comment: C: package ‘org.At.tair.db’ could not be loaded
... Thank you very much Sir ...
written 13 months ago by rkp0
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package ‘org.At.tair.db’ could not be loaded
... library(ath1121501.db) Loading required package: org.At.tair.db Error : .onLoad failed in loadNamespace() for 'org.At.tair.db', details:   call: match.arg(synchronous, c("off", "normal", "full"))   error: 'arg' must be NULL or a character vector Error: package ‘org.At.tair.db’ could not be loaded   ...
microarray written 13 months ago by rkp0 • updated 13 months ago by Martin Morgan ♦♦ 19k

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