Hi, Kristen, You can find the newest version of edgeR here:
http://bioconductor.org/help/bioc-views/2.8/bioc/html/edgeR.html You can either manually install edgeR 2.1.4 or use the biocLite function if you are using R 2.13. Chao-Jen ----- Original Message ----- From: "kristen dang" <[email protected]> To: [email protected] Cc: [email protected], [email protected] Sent: Monday, January 3, 2011 9:45:51 AM Subject: [Bioc-sig-seq] error msg from edgeR estimateCRDisp Dear Gordon, Many thanks for your reply. I apologize, but I cannot find where to download version 2.0.3 of edgeR. I can only find 2.0.2 on the bioconductor site. Would you point me to the appropriate location? Thank you for suggesting the rounding -- I had forgotten that the count data provided to me included decimals. However, after adding the rounding, I get a new error from the estimateCRDisp function: > data = readDGE(targets) > data$counts = round(data$counts) > data = calcNormFactors(data) > contrasts(targets$factor_a) = contr.sum(2) > contrasts(targets$factor_b) = contr.sum(2) > design = model.matrix(~factor_a + factor_b, data = targets) > data.cd = estimateCRDisp(data, design) Error in chol.default(crossprod(design, .vecmat(mu[i, ]/(1 + dispersion * : the leading minor of order 4 is not positive definite > traceback() 5: .Call("La_chol", as.matrix(x), PACKAGE = "base") 4: chol.default(crossprod(design, .vecmat(mu[i, ]/(1 + dispersion * mu[i, ]), design))) 3: chol(crossprod(design, .vecmat(mu[i, ]/(1 + dispersion * mu[i, ]), design))) 2: adjustedProfileLik(spline.disp[i], y.filt, design = design, offset = offset.mat.filt + lib.size.mat.filt) 1: estimateCRDisp(data, design) > Any suggestions are much appreciated. Regards, Kristen Dang message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited. _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing -- Chao-Jen Wong Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., M1-B514 PO Box 19024 Seattle, WA 98109 206.667.4485 [email protected] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
