User: rkp

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rkp0
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Posts by rkp

<prev • 15 results • page 1 of 2 • next >
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Fold Change and LogFC
... Hi everyone, What is the difference between Fold Change and LogFC?. Why it is important? Thanking you. Kind regards, ...
microarray limma written 21 months ago by rkp0 • updated 21 months ago by James W. MacDonald51k
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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 2.4 years ago by rkp0 • updated 2.4 years ago by James W. MacDonald51k
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Answer: A: Identification of DEGs through limma analysis
... Thank you so much Sir   ...
written 2.4 years 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 2.4 years 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 2.4 years ago by rkp0 • updated 2.4 years ago by Aaron Lun25k
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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 2.8 years 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 2.8 years 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 2.8 years 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 2.8 years ago by rkp0 • updated 2.8 years ago by Gordon Smyth39k
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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 2.8 years ago by rkp0

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Popular Question 21 months ago, created a question with more than 1,000 views. For Heatmap error: 'ColSideColors' must be a character vector of length ncol(x)

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