User: Matt McCall

gravatar for Matt McCall
Matt McCall50
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50
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New User
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Last seen:
14 years, 11 months ago
Joined:
15 years, 1 month ago
Email:
m******@mail.nih.gov

Posts by Matt McCall

<prev • 5 results • page 1 of 1 • next >
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limma object column subsetting
... In the old limma, one could subset a MAlist or RGlist (let's say RGnorm is a MAlist) by entering: RGnorm[,1:3] for the first three columns for example In the version, I'm using now (v1.8.1) this no longer works. > RGnorm[,1] Error in object$targets[j, , drop = FALSE] : incorrect number ...
limma written 14.9 years ago by Matt McCall50 • updated 14.9 years ago by Gordon Smyth39k
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Tcl install
... I'm trying to install widgetTools (because genefilter requires it) and it says that Tcl wasn't installed properly, but I have Tcl installed and I've even tried telling R where it is: R CMD INSTALL --configure-args="--with-tcl- include=/sw/include/tcl8.4 --with-tcl-lib=/sw/lib/tcl8.4" -l ~/Library/ ...
genefilter widgettools written 15.1 years ago by Matt McCall50
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Problem installing graph package
... Using R v2.0.0 on MacOS X in the R console. I was able to install most of bioconductor. I wanted to use the GOstats package (amoung a few others), and it didn't install properly. So I went back to try to find the problem, and it seems that the graph package isn't installing. Any suggestions? Matt ...
ruuid rhdf5 graph hexbin rgraphviz written 15.1 years ago by Matt McCall50 • updated 15.1 years ago by rgentleman5.5k
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Comment: C: contrasts.fit Error
... I updated my version and still get the same error. Here is the model matrix if that helps: cln.mm A B C D E F H I J 1 0 0 0 1 0 1 0 0 0 2 0 0 0 1 1 0 0 0 0 3 1 0 0 0 0 1 0 0 0 4 0 0 1 0 0 0 0 1 0 5 0 0 1 0 0 0 0 1 0 6 0 0 0 1 0 1 0 0 0 7 1 0 0 0 1 0 0 0 0 8 0 0 0 1 1 0 0 0 0 9 ...
written 15.2 years ago by Matt McCall50
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contrasts.fit Error
... When I try to run the following line of code: cln.fit2 <- contrasts.fit(cln.fit, cln.cm) where cln.fit comes from: cln.fit <- lmFit(colon$M, cln.mm) where colon is a limma object and cln.mm is the model matrix. also cln.cm is the contrast matrix from: cln.cm <- makeContrasts(MSLiver-MSLung, ...
microarray colon limma written 15.2 years ago by Matt McCall50 • updated 15.2 years ago by Gordon Smyth39k

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