User: Ekta Jain

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Ekta Jain370
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Posts by Ekta Jain

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edgeR: topTags
... Hi KJ Lim, Once you have your row names of interest i.e up-regulated or down- regulated genes you can easily fetch other information for those row names. For instance the results from limma link back to samples by heatmaps. A heat map of upregulated genes: >expVal<-(eset[geneList,]) # Assuming ...
limma edger written 5.5 years ago by Ekta Jain370 • updated 5.5 years ago by KJ Lim420
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Comment: C: edgeR: topTags
... Hi KJ Lim, To get the gene lists for up-regulated genes, you could try > geneList<-which(de[,1] == 1) ## if you have two contrasts > geneList<-which(de[,1] == 1 & de[,2] == 1) Changing '1' to '-1' will give down-regulated genes. Hope this helps. Best, Ekta -----Original Message- ...
written 5.5 years ago by Ekta Jain370
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Comment: C: Extracting topTable data from saved file
... Hi Avoks, The toptable is generated from your fit object. In LIMMA, you would need an object for the Venn Diagram function (http://127.0.0.1:22029/library/limma/html/venn.html) this in your case should be a vennCounts or decideTests(fit). But if you do not have access to your fit object and only ha ...
written 5.5 years ago by Ekta Jain370
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Comment: C: Moderated t-test
... Hi Chintanu, Sorry I went underground for a short time., not sure if you have solved your problem but sharing some info here incase it helps. If you sort your toptable in R it will sort everything except the row names. If you fit the annotation on your data before you do toptable it will sort all ...
written 5.5 years ago by Ekta Jain370
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Answer: A: Extracting topTable data from saved file
... Hi Avoks, What you are looking for is the decideTests(). Assuming 'fit' is your LIMMA fit object, something like: > Results <- decideTests(fit) # gives you counts of upregulated(1) and downregulated(-1) genes in each comparison. Kindly note that default cut-off for LogFC =0, this can be change ...
written 5.5 years ago by Ekta Jain370
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Comment: C: LIMMA decideTests result zero from contrast matrix
... Dear Alex, Thank you very much. It appears much clear now. I agree, I wouldn't want to apply the filter to unadjusted P values since it just shows that the results obtained are very insignificant. I did not understand in detail how the decideTests() works and was looking for some info regarding the ...
written 5.5 years ago by Ekta Jain370
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Comment: C: Moderated t-test
... Hi, The cbind function combines data frames column wise - you should read here http://www.stat.ucl.ac.be/ISdidactique/Rhelp/library/base/html/cb ind.html Or >?cbind on your R console. Toptable will only give you the a subset of the entire data i.e the top genes in which genes are ranked accordin ...
written 5.5 years ago by Ekta Jain370
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Answer: A: Moderated t-test
... Hi Chintanu, You can use the cbind function. > toptableOut<- topTable(fit2, number=Inf, adjust.method="BH")$t > x <- cbind(file[,1],toptableOut) ## the (file[,1] will get you all rows for column 1 > write.table(x,".txt", quote=F, row.names=FALSE, sep="\t") Hope this helps, Ekta --- ...
written 5.5 years ago by Ekta Jain370
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Comment: C: LIMMA decideTests result zero from contrast matrix
... Dear Jim, I did change things around when you pointed out for the first time. All I have been doing is > numGenes <- rownames(eset) > topTable(fit2, coef=1, adjust="BH", sort.by="B", number=numGenes) And > results<-decideTests(fit2, method ="global", lfc =0) As you mention in your ema ...
written 5.5 years ago by Ekta Jain370
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Comment: C: LIMMA decideTests result zero from contrast matrix
... Hi Steve, Definitely not annoy people here on. I am being given help, which is nice. Apologies for the same. I wouldn't completely rely on Wikipedia, ever :) I am a warm person. Yes, (x,...) is generated from decideTests(fit). The summary(decideTests, lfc=0, method="separate",adjust.method="BH",p ...
written 5.5 years ago by Ekta Jain370

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