User: Mete Civelek

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Mete Civelek180
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Posts by Mete Civelek

<prev • 18 results • page 1 of 2 • next >
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Comment: C: lmFit: Error in dimnames(fit$cov.coefficients)
... Dear Gordon, Upgrading to the current release of limma solved the problem. I do not get error messages now. Thank you very much for your help. Mete -----Original Message----- From: Gordon K Smyth [mailto:smyth@wehi.EDU.AU] Sent: Monday, November 18, 2013 2:49 PM To: Mete Civelek Cc: Bioconductor ...
written 6.0 years ago by Mete Civelek180
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Comment: C: lmFit: Error in dimnames(fit$cov.coefficients)
... Dear Gordon, Thank you for the quick response. The reason I am not updating the design matrix is because it is already removing the NA's in the continuous variable predictor. I am doing the METSIMData[,i] to remove the individuals with the missing phenotypes so as to match the individuals in the de ...
written 6.0 years ago by Mete Civelek180
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lmFit: Error in dimnames(fit$cov.coefficients)
... Dear All, I am getting an error when trying to do an analysis with the lmFit function in the limma package. I can't get a handle at what the problem might be. I will appreciate any insights you can provide. Thank you Mete library(limma) memory.size(max = TRUE) MData<-read.delim("MData.txt", he ...
limma written 6.0 years ago by Mete Civelek180 • updated 6.0 years ago by Gordon Smyth39k
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Comment: C: How to deal with Affymetrix probe that map to multiple genes
... Discarding probes that map to multiple unique gene symbols would be my suggestion. There is no way to know which gene expression the probeset is measuring. -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Gundala Viswana ...
written 6.2 years ago by Mete Civelek180
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Comment: C: How to deal with Affymetrix probe that map to multiple genes
... Discarding probes that map to multiple unique gene symbols would be my suggestion. There is no way to know which gene expression the probeset is measuring. -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Gundala Viswana ...
written 6.2 years ago by Mete Civelek180
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Comment: C: Problem installing genefilter (Ubuntu 12.04; Bioconductor v2.12)
... Hi All, I have microarray data from more than 1,000 people. I am interested in removing some "batch effects/adjustment variables and then correlating the expression of the genes with multiple phenotypes measured in these people. The phenotypes are continuous variables such as body mass index and cho ...
written 6.3 years ago by Mete Civelek180
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Comment: C: RNAseq data normalization without differential expression
... Hi Mike, Thank you for the suggestions. I will try out the log transformation function. Mete -------- Original message -------- From: Michael Love Date: To: "Civelek, Mete" Cc: bioconductor at r-project.org Subject: Re: [BioC] RNAseq data normalization without differential expression hi Mete, ...
written 6.3 years ago by Mete Civelek180
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RNAseq data normalization without differential expression
... Dear All, I have RNAseq counts for 400 human donors. This is a random sampling of human subjects from a population-wide study. I am not interested in differential expression of genes between certain groups. There are differences in sequence reads because of library size therefore I need to normaliz ...
rnaseq normalization edger deseq written 6.3 years ago by Mete Civelek180 • updated 6.3 years ago by Michael Love26k
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Answer: A: [R] Select single probe-set with median expression from multiple probe-sets corr
... Hi Atul, Not sure if there is a function in affy or limma for what you are trying to do but this might help:http://www.inside-r.org/packages/cran/WGCNA/docs/collapseRows Mete On Apr 3, 2013, at 9:17 PM, Atul Kakrana > wrote: Hello Martin and All, I think I was not clear with my question an ...
written 6.6 years ago by Mete Civelek180
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Answer: A: Linkage Disequilibrium Analysis
... Not sure about a Bioconductor package but you can try Haploview from Broad Institute. -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Ovokeraye Achinike-Oduaran Sent: Thursday, July 05, 2012 2:58 PM To: bioconductor at ...
written 7.4 years ago by Mete Civelek180

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Popular Question 6.0 years ago, created a question with more than 1,000 views. For lmFit: Error in dimnames(fit$cov.coefficients)

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