error in decideTests(fit2)?

Question

[jaizebrafish]

I am trying to follow this tutorial https://rawgit.com/bioinformatics-core-shared-training/microarray-analysis/master/de-tutorial.html, to analyze microarray data, everything works perfectly until the step "decideTests(fit2)". As I run this step, it shows some strange error.

ERROR while rich displaying an object: Error in `[.TestResults`(a, part_r$start, , drop = FALSE): unused argument (drop = FALSE)

Traceback:
1. FUN(X[[i]], ...)
2. tryCatch(withCallingHandlers({
 .     if (!mime %in% names(repr::mime2repr)) 
 .         stop("No repr_* for mimetype ", mime, " in repr::mime2repr")
 .     rpr <- repr::mime2repr[[mime]](obj)
 .     if (is.null(rpr)) 
 .         return(NULL)
 .     prepare_content(is.raw(rpr), rpr)
 . }, error = error_handler), error = outer_handler)
3. tryCatchList(expr, classes, parentenv, handlers)
4. tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. doTryCatch(return(expr), name, parentenv, handler)
6. withCallingHandlers({
 .     if (!mime %in% names(repr::mime2repr)) 
 .         stop("No repr_* for mimetype ", mime, " in repr::mime2repr")
 .     rpr <- repr::mime2repr[[mime]](obj)
 .     if (is.null(rpr)) 
 .         return(NULL)
 .     prepare_content(is.raw(rpr), rpr)
 . }, error = error_handler)
7. repr::mime2repr[[mime]](obj)
8. repr_text.matrix(obj)
9. ellip_limit_arr(obj, rows, cols)
10. arr_partition(a, rows, cols)
11. structure(list(upper = a[part_r$start, , drop = FALSE], lower = a[part_r$end, 
  .     , drop = FALSE]), omit = "rows")
12. a[part_r$start, , drop = FALSE]

I tried to figure out the error as if there are any missing values using "sumis.na(df))" but I am not able to figure out the reasons behind this error.

Answer 1

[Gordon Smyth]

I just ran the tutorial you link to just now using the current versions of R and Bioconductor and it runs ok.

There are a couple of problems with the tutorial: the ncbi ftp url appears to have changed, the rowttests() command fails. Also I recommend against the use of varFilter(). However all the limma differential expression steps including decideTests(fit2) work perfectly.

The error and the traceback shows that you are trying to display the output from decideTests(fit2) using other code that is not part of the tutorial itself. The code is trying to subset the output of decideTests(fit2) using drop=FALSE, but that indeed is not currently allowed. If you type help("[.TestResults") you'll see that drop is not a possible argument.