The way the sample data is provided is not useful. I have re-built your data, please find the dput() version below (and pls check whether I got it right...).
This is not my area of competence at all, but from what I see from the help page is that the expected parameters are, among others: x A matrix or dataframe y A second matrix or dataframe __with the same number of rows as x__ I hope that somebody with a better understanding of your intention is able to pick up from here, with the sample data in useful format. Rgds, Rainer dput( genes ) structure(list(Genes = structure(1:10, .Label = c("KCNAB3", "KCNB1", "KCNB2", "KERA", "KGFLP1", "KGFLP2", "KHDC1", "KHDC1L", "KHDC3L", "KHDRBS1"), class = "factor"), Cell.line1 = c(12.02005181, 0.02457449, 0.44791862, 0.06090217, 0.02450101, 0, 0, 2.3189445, 0, 0), Cell.line2 = c(11.140091, 1.3028535, 0.1060137, 0, 0, 0, 0, 2.8252262, 0, 0), Cell.line3 = c(15.60381163, 0.81538294, 0.09864136, 0.03352993, 0, 0, 0, 5.29099724, 0, 0 ), Cell.line4 = c(13.44151596, 0.59318327, 0, 0.03634781, 0, 0, 0, 7.44183228, 0, 0), Cell.line5 = c(25.3716103, 0.15332321, 0, 0.04190912, 0, 0, 0, 1.94629741, 0, 0), Cell.line6 = c(8.12373424, 4.18181234, 0.05857207, 0, 0.02563099, 0, 0, 8.56022436, 0, 0 ), Cell.line7 = c(7.67506261, 1.65268403, 0.05945414, 0, 0.03902548, 0, 0, 7.50838343, 0, 0.0308118), Cell.line8 = c(24.43776341, 5.9834632, 0.20733924, 0.07752608, 0, 0, 0, 7.17964645, 0, 0), Cell.line9 = c(18.33244818, 1.51423807, 0.05830982, 0.01585643, 0, 0, 0, 3.28602729, 0, 0), Cell.line10 = c(9.224225, 0, 0, 16.664245, 0, 0, 0, 0, 3.598534, 2.600173)), .Names = c("Genes", "Cell.line1", "Cell.line2", "Cell.line3", "Cell.line4", "Cell.line5", "Cell.line6", "Cell.line7", "Cell.line8", "Cell.line9", "Cell.line10" ), row.names = c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10"), class = "data.frame") dput( features ) structure(list(Cell.line = c("Growth rate", "Drug sensitivity" ), Cell.line1 = c(NA, "41.33"), Cell.line2 = c(NA, "26.76"), Cell.line3 = c(NA, "24.19"), Cell.line4 = c("51.41", NA), Cell.line5 = c(NA_character_, NA_character_), Cell.line6 = c("5.03", "1.40"), Cell.line7 = c("6.57", "1.88"), Cell.line8 = c("8", "1.33"), Cell.line9 = c("1.26", "5.05"), Cell.line10 = c("3", "9.12")), .Names = c("Cell.line", "Cell.line1", "Cell.line2", "Cell.line3", "Cell.line4", "Cell.line5", "Cell.line6", "Cell.line7", "Cell.line8", "Cell.line9", "Cell.line10"), row.names = c(NA, -2L), class = "data.frame") On Thu June 18 2015 10:19:55 Sarah Bazzocco wrote: > This post was called "help" before, I changed the Subject. > Thanks for the comments. > Here the example: (I have the two lists saved as .csv and I can open them in > R) > > Sheet one- Genes (10 genes expression, not binary, meaured in 10 cell lines) > > genes > Genes Cell.line1 Cell.line2 Cell.line3 Cell.line4 Cell.line5 > 1 KCNAB3 12.02005181 11.1400910 15.60381163 13.44151596 25.37161030 > 2 KCNB1 0.02457449 1.3028535 0.81538294 0.59318327 0.15332321 > 3 KCNB2 0.44791862 0.1060137 0.09864136 0.00000000 0.00000000 > 4 KERA 0.06090217 0.0000000 0.03352993 0.03634781 0.04190912 > 5 KGFLP1 0.02450101 0.0000000 0.00000000 0.00000000 0.00000000 > 6 KGFLP2 0.00000000 0.0000000 0.00000000 0.00000000 0.00000000 > 7 KHDC1 0.00000000 0.0000000 0.00000000 0.00000000 0.00000000 > 8 KHDC1L 2.31894450 2.8252262 5.29099724 7.44183228 1.94629741 > 9 KHDC3L 0.00000000 0.0000000 0.00000000 0.00000000 0.00000000 > 10 KHDRBS1 0.00000000 0.0000000 0.00000000 0.00000000 0.00000000 > Cell.line6 Cell.line7 Cell.line8 Cell.line9 Cell.line10 > 1 8.12373424 7.67506261 24.43776341 18.33244818 9.224225 > 2 4.18181234 1.65268403 5.98346320 1.51423807 0.000000 > 3 0.05857207 0.05945414 0.20733924 0.05830982 0.000000 > 4 0.00000000 0.00000000 0.07752608 0.01585643 16.664245 > 5 0.02563099 0.03902548 0.00000000 0.00000000 0.000000 > 6 0.00000000 0.00000000 0.00000000 0.00000000 0.000000 > 7 0.00000000 0.00000000 0.00000000 0.00000000 0.000000 > 8 8.56022436 7.50838343 7.17964645 3.28602729 0.000000 > 9 0.00000000 0.00000000 0.00000000 0.00000000 3.598534 > 10 0.00000000 0.03081180 0.00000000 0.00000000 2.600173 > > Sheet two - features (2 features(Growth rate,drug sensitivity for 10 cell > lines) > > features > Cell.line Cell.line1 Cell.line2 Cell.line3 Cell.line4 Cell.line5 > 1 Growth rate NA NA NA 51.41 NA > 2 Drug sensitivity 5.03 6.57 8 1.26 3 > Cell.line6 Cell.line7 Cell.line8 Cell.line9 Cell.line10 > 1 41.33 26.76 24.19 NA NA > 2 1.40 1.88 1.33 5.05 9.12 > > What I found: > corr.test {psych} > corr.test(x, y = NULL, use = > "pairwise",method="pearson",adjust="BH",alpha=.01) > --> I adjusted the original command to what I need (BH insted og holm) and > alpha=.01 insted of 0.05. > > I would be very happy, if someone could show me how to use this command, in > particular how to refer as x and y to the two sheets I have (Genes and > Features). I would take it from there. > > Thanks a lot in advance. > > Sarah ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.