Dear all, There is something that is puzzling me. I am trying to create an html page with some results I have. These are the 42 LocusID entries: > mylistLI $"1554018_at" [1] 10457 $"1566557_at" [1] 440465 $"202270_at" [1] 2633 $"202555_s_at" [1] 4638 $"202637_s_at" [1] 3383 $"202748_at" [1] 2634 $"203717_at" [1] 1803 $"204181_s_at" [1] 23099 $"204806_x_at" [1] 3134 $"204963_at" [1] 8082 $"205170_at" [1] 6773 $"205227_at" [1] 3556 $"206544_x_at" [1] 6595 $"210785_s_at" [1] 9473 $"211478_s_at" [1] 1803 $"211965_at" [1] 677 $"212959_s_at" [1] 79158 $"213645_at" [1] 55556 $"214978_s_at" [1] 8497 $"217234_s_at" [1] 7430 $"218136_s_at" [1] 51312 $"218211_s_at" [1] 79083 $"219872_at" [1] 51313 $"221920_s_at" [1] 51312 $"221986_s_at" [1] 54800 $"223495_at" [1] 83987 $"223679_at" [1] 1499 $"224823_at" [1] 4638 $"225051_at" [1] 2035 $"225564_at" [1] 221178 $"226001_at" [1] 51088 $"226363_at" [1] 10057 $"226676_at" [1] 25925 $"227565_at" [1] 51088 $"227741_at" [1] 201562 $"228030_at" [1] 10180 $"229441_at" [1] 8322 $"231721_at" [1] 83700 $"232898_at" [1] 1601 $"236488_s_at" [1] 440259 $"241359_at" [1] NA $"243041_s_at" [1] 27303 When I try: >htmlpage(mylistLI, filename = "mylist.html", title = "mylist", table.center = TRUE) I obtain an html page with just the first entry: Differentially Expressed Genes mylist 10457 However, if I do >htmlpage(1:42, filename = "mylist.html", title = "mylist", table.center = TRUE) I obtain, as expected: Differentially Expressed Genes mylist 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 I have read the help available through ?htmlpage but could not find the likely cause - I admit my R knowledge is very poor. It seems to me I'm missing something extremely easy and if so, please excuse my ignorance. Could you help me? I wasn't sure whether this was a posting for R or BioC. If you consider I got it wrong, I apologize in advance. I have just installed R 2.0.1, BioConductor 1.5 and I'm using Windows XP Thanks in advance, Fatima -- No virus found in this outgoing message. Checked by AVG Anti-Virus.

Fatima Nunez wrote: > Dear all, > > There is something that is puzzling me. I am trying to create an html page > with some results I have. These are the 42 LocusID entries: > Hi Fatima, The problem here is you are passing a list with 42 LocusIDs, rather than a list containing a character vector of those locus ids. From the help page: genelist: A list of character vectors containing ids to be made into hypertext links. See details for more information. So mylistLI should look like this: > mylistLI $ll [1] 10457 440465 2633 4638 etc You could convert mylistLI to what you need by mylistLI <- list(ll = unlist(mylistLI)) In addition, you should pass a repository list, because without doing so you are relying on the default being correct. >htmlpage(mylistLI, filename = "mylist.html", title = "mylist", table.center = TRUE, repository=list("ll")) Also note that LocusLink has been deprecated, so you might want to use >htmlpage(mylistLI, filename = "mylist.html", title = "mylist", table.center = TRUE, repository=list("en")) Which will build links to EntrezGene. For this you will need the devel version of annotate. HTH, Jim -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623