... You need to become familiar with the help system, and to check there to ensure you are doing things correctly. From `?getMainProbes`, we have:
getMainProbes(input, level = "core")
input: Either a character string (e.g., "pd.hugene.1.0.st.v1") or a
... Have you read the [vignette]? You can just as easily get data from the GSE entry, or if you want the raw data you can use `getGEOSuppFiles`. I have personally never used the pipeline you outline, opting instead for getting the GSE directly.
: http://bioconductor.org/packages/release/bioc/v ...
... It's better if you give all of the R output rather than what you think might be useful. This error often comes up if you are missing the xml headers, so you probably have to install libxml2-devel. Often there is something like
checking for pkg-config...
/usr/bin/pkg-config checking for xml2-c ...
... You can get data for that organism from the `AnnotationHub`:
> hub <- AnnotationHub()
> query(hub, c("olea europaea", "orgdb"))
AnnotationHub with 3 records
# snapshotDate(): 2018-10-24
# $dataprovider: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# $species: Olea ...
... This isn't a Bioconductor question! None of the packages you mention are part of Bioconductor. In future you should ask questions about basic R stuff on firstname.lastname@example.org
That said, the packages you mention are all in the set of *recommended packages*, and if you installed R as a privileged user ...
... Have you read the help page for `test_diff`? It says:
A SummarizedExperiment object containing FDR estimates of differential expression
And FDR is generally assumed to mean Benjamini and Hochberg's method (for example, if you ask `p.adjust` to use `fdr`, you get `BH`). ...