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 4 days ago by rkp0 • updated 4 days ago by James W. MacDonald45k
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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 7 months ago by rkp0 • updated 7 months ago by James W. MacDonald45k
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Answer: A: Identification of DEGs through limma analysis
... Thank you so much Sir   ...
written 7 months 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 8 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 8 months ago by rkp0 • updated 8 months ago by Aaron Lun18k
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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 13 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 13 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 13 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 13 months ago by rkp0 • updated 13 months ago by Gordon Smyth32k
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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 13 months ago by rkp0

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