While running DEseq for DGE, I am facing following problem. Error in preplot.locfit.raw(object, newdata, where, what, band) : NA/NaN/Inf in foreign function call (arg 2) Calls: estimateDispersions ... predict.locfit -> preplot.locfit -> preplot.locfit.raw -> .C In addition: Warning messages: 1: In lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth, : compparcomp: perfect fit 2: In lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth, : procv: parameters out of bounds 3: In lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth, : max_nr not converged Execution halted My file does not contain any "NA or empty cells", I have tried every possible thing but still not able to find the problem behind this error. Kindly suggest me some solution for this. Waiting for your positive response. -- output of sessionInfo(): > sessionInfo() R version 3.0.3 (2014-03-06) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- Sent via the guest posting facility at bioconductor.org.

Hi It is hard to give you advise given the terse information in your post. Please read the posting guide. In particular, please post the complete code including (reasonably truncated) output that led you to the error and the output of sessionInfo as it is _after_ you ran your commands. Also, maybe switching to DESeq2 solves the issue? We strongly recommend that the old DESeq package is used only for ongoing projects, and all new projects be done with DESeq2. simon On 03/07/14 11:40, nisha [guest] wrote: > While running DEseq for DGE, I am facing following problem. > > Error in preplot.locfit.raw(object, newdata, where, what, band) : > NA/NaN/Inf in foreign function call (arg 2) > Calls: estimateDispersions ... predict.locfit -> preplot.locfit -> preplot.locfit.raw -> .C > In addition: Warning messages: > 1: In lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth, : > compparcomp: perfect fit > 2: In lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth, : > procv: parameters out of bounds > 3: In lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth, : > max_nr not converged > Execution halted > > My file does not contain any "NA or empty cells", I have tried every possible thing but still not able to find the problem behind this error. Kindly suggest me some solution for this. Waiting for your positive response. > > -- output of sessionInfo(): > >> sessionInfo() > R version 3.0.3 (2014-03-06) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 >