I am trying to access data for all 404 samples in the GEO entry GSE120742 using GEOquery on R. My steps are,
library(GEOquery) eData <- getGEO("GSE120742") expr <- eData[] exprs[expr]
Now, when I do this, I get "expr" as
$GSE120742_series_matrix.txt.gz ExpressionSet (storageMode: lockedEnvironment) assayData: 0 features, 404 samples - Notice this element names: exprs protocolData: none phenoData sampleNames: GSM3409642 GSM3409643 ... GSM3410057 (404 total) varLabels: title geo_accession ... tissue:ch1 (47 total) varMetadata: labelDescription featureData: none experimentData: use 'experimentData(object)' pubMedIds: 30464211 Annotation: GPL16791
And exprs(expr) as
GSM3409642 GSM3409643 GSM3409644 GSM3409645 GSM3409646 # ... (that is, just sample names and no numeric data)
I thought this might be because the experiment is a mix of ChIP-seq and RNA-seq data. Indeed, for other examples in the vignette, they are able to do
exprs[...] to get a matrix with actual values (maybe their experiments are on a single platform)?
However, I am therefore not sure how I can get data for this experiment, for ALL 404 samples, without downloading the supplementary files. Any ideas?
Maybe you cannot do this in R. Note: Don't feed the trolls.
That's not an answer, nor helpful. Please put some effort.
I think this is enough effort from me. My effort has spurred your effort as this question has not been answered for three days, so that is all the effort that was required.
That isn't how the forum works.
If the thread hasn't obtained any attention in 3 days, that's just the nature of the beast. It is not a license to make flippant comments.
"There was no answer so I gave a wrong answer which made a responsible person step in and correct me, so I am right in what I did" is such a crappy stance to take.