Thanks Peter and Aaron. For SummarizedExperiment 1.1.9 in svn now:
For Aaron's original issue, SummarizedExperiment now allows construction from NULL colnames; it does not construct colnames. The behavior of SummarizedExperiment with respect to colnames is to use and keep them if provided, but not to add colnames to assays if they are absent -- they are provided in the constructor to se2, so present in the assay in se2. The inconsistency between assay colnames and colData rownames in the constrution of se3 is now (and should have been before) an error. > assay = matrix(0, 2, 3, dimnames=list(NULL, LETTERS[1:3])) > colData = DataFrame(row.names=letters[1:3]) > SummarizedExperiment(assay, colData=colData) Error in FUN(X[[i]], ...) : assay colnames() must be NULL or equal colData rownames() Thanks for the feed back / bug reports; please let me know if there are additional issues. ________________________________________ From: Peter Hickey [[email protected]] Sent: Sunday, December 06, 2015 7:56 PM To: Morgan, Martin Cc: [email protected]; [email protected] Subject: Re: do SummarizedExperiments really need colnames? While on the topic of SummarizedExperiment colnames, the circumstances in which these are stripped from the assays and overridden by colData is confusing to me, particularly case 2 below (a warning in case 3 might be useful too). > m1 <- matrix(1:10, ncol = 2) > m2 <- m1 > colnames(m2) <- c("A", "B") > > se1 <- SummarizedExperiment(m1, colData = DataFrame(row.names = c("A", "B"))) > se2 <- SummarizedExperiment(m2) > se3 <- SummarizedExperiment(m2, colData = DataFrame(row.names = c("C", "D"))) > > # colnames correctly set to c("A", "B") and stripped from assays > colnames(se1) [1] "A" "B" > se1@assays[[1]] [,1] [,2] [1,] 1 6 [2,] 2 7 [3,] 3 8 [4,] 4 9 [5,] 5 10 > # colnames correctly set to c("A", "B") set and but not stripped from assays > colnames(se2) [1] "A" "B" > se2@assays[[1]] A B [1,] 1 6 [2,] 2 7 [3,] 3 8 [4,] 4 9 [5,] 5 10 > # colnames set to c("C", "D") (without warning about mismatch) and stripped > # from assays > se3@assays[[1]] [,1] [,2] [1,] 1 6 [2,] 2 7 [3,] 3 8 [4,] 4 9 [5,] 5 10 > sessionInfo() R Under development (unstable) (2015-11-28 r69714) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.5 (Yosemite) locale: [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8 attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] SummarizedExperiment_1.1.5 Biobase_2.31.1 [3] GenomicRanges_1.23.4 GenomeInfoDb_1.7.3 [5] IRanges_2.5.9 S4Vectors_0.9.11 [7] BiocGenerics_0.17.2 loaded via a namespace (and not attached): [1] zlibbioc_1.17.0 XVector_0.11.1 This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
