[Bioc-devel] strange bug in a BioC workflow that only appears on Jenkis

Bernd Klaus bernd.klaus at embl.de
Thu Dec 3 12:41:51 CET 2015

Dear all,

I am currently developing an end-to-end workflow for Microarray

In this workflow I download some clinical microarray 
data from arrayExpress (CEL files), 
import it with oligo, annotate it using the
appropriate ChipDB and then obtain 
results with limma. This gives me a data.frame "tableC" with
the results from limma.

The data set contains paired inflammed/non-inflamed (I/nI) mucosa
samples from patients with Chron's diseaese(C) or ulcerative colitis

In the workflow I only analyse the differences between I/nI samples
within the patients in C and obtain a limma results table called

I then want to extract the probeset IDs of
the DE genes like so:

DEgenesCD <- rownames(base::subset(tableC, adj.P.Val < 0.1))

Now, on my local computer(s) this gives me something like

# message(paste0(as.character(DEgenesCD)[1:5], collapse = "--"))
# > 7928695--8123695--8164535--8009746--7952249

However, on the CI system I get 

# > NA--NA--NA--NA--NA

So it seems that the content of tableC "dissapears" somehow.
See e.g.

The minimal dummy workflow that has the bug is here in the svn

Now strangely enough, if I run it on my local machine, save the
expression data as an RData object, submit this object to svn and the
load the pre-saved object in the workflow it builds successfully.

So my best guess is that there is something unusual happening during
the creation of the eSet from the downloaded data that then somehow
affects the result table from limma.

I have been trying to chase this bug for ca. three weeks, so any input
would be very much appreciated ...

Thanks and best wishes,


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