User: rkp

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rkp0
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Posts by rkp

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Annotation of Probe id to Gene
... Why some probes have "NA" for SYMBOL but having ENTREZID as well as the TAIR accession number and what can I do when single probe having more than one GENE SYMBOL, ENTREZID and TAIR Accession. Kindly suggest on below table. Which gene from the probe id 263153_s_at, I can select for further studies? ...
microarray arabidopsis thaliana annotate bioconductor written 12 weeks ago by rkp0 • updated 12 weeks ago by James W. MacDonald44k
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Answer: A: Identification of DEGs through limma analysis
... Thank you so much Sir   ...
written 12 weeks ago by rkp0
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Identification of DEGs through limma analysis
... I wish to analyze microarray data for identification of DEGs through limma analysis at the threshold P<0.05 or a fold change >1.5. I written R script as  results<-decideTests(fit2, p.value=0.05) or results<-decideTests(fit2, lfc=1.5) When I run these script, get some variation in the ...
microarray limma p values lfc degs written 3 months ago by rkp0
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How to extract DEG using limma at threshold value p<0.05 and fold change >1.5 ?
... How to extract top DEG using limma at threshold value p<0.05 and fold change >1.5 ? I request you all too kindly suggest the R script for topTable. topTable(fit2, coef=2, ……?????????) Thanking you.   ...
microarray limma R bioconductor written 3 months ago by rkp0 • updated 3 months ago by Aaron Lun16k
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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 8 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 8 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 8 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 8 months ago by rkp0 • updated 8 months ago by Gordon Smyth31k
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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 8 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 8 months ago by rkp0 • updated 8 months ago by Gordon Smyth31k

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