Question: [Limma] Calculate the relation between mRNA and miRNA
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gravatar for yao chen
7.5 years ago by
yao chen200
yao chen200 wrote:
Hi all, I have a problem to use lmFit calculated the correlation between mRNA and miRNA, because my miRNA data contained "NA" values. So if I use :lmFit(mRNA,miRNA), I got the message "Error in qr.default(x) : NA/NaN/Inf in foreign function call (arg 1)". The original "lm" function allow to included "NA", why lmFit can't? Thanks, Jack [[alternative HTML version deleted]]
mirna • 543 views
ADD COMMENTlink modified 7.5 years ago by Belinda Phipson130 • written 7.5 years ago by yao chen200
Answer: [Limma] Calculate the relation between mRNA and miRNA
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gravatar for Belinda Phipson
7.5 years ago by
Belinda Phipson130 wrote:
Hi Jack I think you have misunderstood what lmFit does. lmFit takes the data object/matrix, call it x, and fits a user-specified design matrix to it, call it design. i.e. > fit <- lmFit(x,design) >From your message I don't understand what format your data is in. However, if you have two vectors, and you wanted to calculate a correlation, you could just use > cor(vector1, vector2, use=complete.obs) which would take care of the missing values. Cheers, Belinda > Hi all, > > I have a problem to use lmFit calculated the correlation between mRNA and > miRNA, because my miRNA data contained "NA" values. > > So if I use :lmFit(mRNA,miRNA), I got the message "Error in qr.default(x) > : > NA/NaN/Inf in foreign function call (arg 1)". > > The original "lm" function allow to included "NA", why lmFit can't? > > Thanks, > > Jack > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
ADD COMMENTlink written 7.5 years ago by Belinda Phipson130
Hi Belinda, I know what you mean. But I also want to include the treatment factor. The linear model is mRNA=miRNA+treatment+miRNA*treatment. So I can't use simple correlation. Jack 2012/6/22 Belinda Phipson <phipson@wehi.edu.au> > Hi Jack > > I think you have misunderstood what lmFit does. lmFit takes the data > object/matrix, call it x, and fits a user-specified design matrix to it, > call it design. i.e. > > > fit <- lmFit(x,design) > > From your message I don't understand what format your data is in. However, > if you have two vectors, and you wanted to calculate a correlation, you > could just use > > > cor(vector1, vector2, use=complete.obs) > > which would take care of the missing values. > > Cheers, > Belinda > > > > > Hi all, > > > > I have a problem to use lmFit calculated the correlation between mRNA and > > miRNA, because my miRNA data contained "NA" values. > > > > So if I use :lmFit(mRNA,miRNA), I got the message "Error in qr.default(x) > > : > > NA/NaN/Inf in foreign function call (arg 1)". > > > > The original "lm" function allow to included "NA", why lmFit can't? > > > > Thanks, > > > > Jack > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:10}}
ADD REPLYlink written 7.5 years ago by yao chen200
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