User: Kripa R

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Kripa R180
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Posts by Kripa R

<prev • 18 results • page 1 of 2 • next >
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Annotate - gene name to ENSEMBL
... Hi everyone, Does anyone know how to go from gene name to ENSEMBL ID? I'm using lumi to analyze my microarray data, however the names get changed from NuID to gene name when reading in the data.... I'd like to do pathway analysis but require either ENSEMBL or GO id format Any help would be greatl ...
microarray go lumi written 4.0 years ago by Kripa R180 • updated 4.0 years ago by Hotz, Hans-Rudolf380
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Comment: C: LIMMA: Error in rowMeans(y$exprs, na.rm=TRUE):'x' must be numeric
... Hi, changing the data to a matrix doesn't help. I think it has something to do with my design matrix which has NAs design <- model.matrix(~0+group, model.frame(~0+group,data, na.action=NULL)) > design[55:65,] group1 group2 55 0 1 56 1 0 57 1 0 58 0 ...
written 5.1 years ago by Kripa R180
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LIMMA: Error in rowMeans(y$exprs, na.rm=TRUE):'x' must be numeric
... Hi so I'm trying to do limma fitting on my data but i keep getting the following error Error in rowMeans(y$exprs, na.rm=TRUE):'x' must be numeric But I'm not sure what the problem is does anyone have suggestions? Here's what i've been doing after normalization: data<-subset(data_pheno, select=i ...
limma written 5.1 years ago by Kripa R180 • updated 5.1 years ago by James W. MacDonald45k
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LIMMA: plotMDS
... Hi again, sorry to be a bother but one more question. After knowing that lets say 20 genes are being used for the PCA would it be possible to figure out how much each gene contributes? So to develop an equation or know specifically in PC1 the variance in these x genes were the most important or som ...
limma written 5.5 years ago by Kripa R180
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limma p-value calculated how?
... Hi, I'm currently using LIMMA to analyze two groups, wt vs treatment group. LIMMA says gene A is significantly different between the two groups, p=10E-6, but when I do a simple t-test I am unable to get such a significant p-value. For example my normalized values for ProbeID:A may be as followed: ...
limma written 5.5 years ago by Kripa R180 • updated 5.5 years ago by David Westergaard280
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Comment: C: LIMMA: plotMDS
... Maybe this is very basic, but how do you identify those 500 genes for the heatmap? .kripa From: amackey@virginia.edu Date: Mon, 7 May 2012 11:47:16 -0400 Subject: Re: [BioC] LIMMA: plotMDS To: kripa777@hotmail.com CC: bioconductor@r-project.org All genes contribute to all principle components; s ...
written 5.5 years ago by Kripa R180
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LIMMA: plotMDS
... Hi I was wondering how I can figure out which genes correspond to each of the principle components ($cmdscale.out). Gene.selection is set to pairwise for the top 500 but I'd like to know exactly which genes are being considered for cmdscale.out[,3], for example. Thanks for the help! .kripa ...
written 5.5 years ago by Kripa R180 • updated 5.5 years ago by Aaron Mackey160
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Answer: A: LIMMA - summarization of Illumina probes for same gene
... Yes, I see what you mean; each illumina probe provides unique information. I guess all the affy summarization options threw me off (avgdiff, liwong, mas, medianpolish, playerout) One thing, the avereps function would be looking for identical ProbeID but would it be possible to change this to look f ...
written 5.7 years ago by Kripa R180
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LIMMA - summarization
... Hi everyone, I'm working on an analysis of illumina microarrays and am using the limma package. But looking at the code provided with the vignette there doesn't seem to be a summarization step (where multiple probes for the same gene are combined) Am I missing something here or would I need to use ...
beadarray written 5.7 years ago by Kripa R180
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Answer: A: simple limma question (read.ilmn)
... No worries, it was a problem on my end. All sorted out now, thanks for the quick response! And yes ill definitely look into updating my R thanks :) Kripa Sent from my BlackBerry? smartphone -----Original Message----- From: Wei Shi Date: Thu, 8 Dec 2011 02:15:00 To: Cc: Subject: Re: [BioC] sim ...
written 6.0 years ago by Kripa R180

Latest awards to Kripa R

Popular Question 4.0 years ago, created a question with more than 1,000 views. For LIMMA: plotMDS
Popular Question 4.0 years ago, created a question with more than 1,000 views. For LIMMA: Error in rowMeans(y$exprs, na.rm=TRUE):'x' must be numeric

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