[Microarray Affymetrix] Issue loading annotation package in read.celfiles() due to incomplete download

[cyouh95]

Description

The following error occurred when rendering Affymetrix.qmd:

Error in oligo::read.celfiles(df_local_paths$`Local Paths`, sampleNames = df_local_paths$`Sample Name`) : 
    The annotation package, pd.mogene.1.0.st.v1, could not be loaded.

read.celfiles() automatically detects and downloads annotation package. Upon further inspection, pd.mogene.1.0.st.v1 is a relatively large file, and the download did not look complete, which seems to be causing the error.

Same issue of incomplete download occurs if manually download using download.file(). Assuming read.celfiles() uses similar method of downloading, the default value for timeout is 60 seconds.

Solution

Set global option to increase timeout in Affymetrix.qmd:

options(timeout=1000)