Question: Retrieving miRNA data from Firehose by using RTCGAToolbox
1
gravatar for dodausp
11 months ago by
dodausp120
Denmark/Copenhagen/BRIC
dodausp120 wrote:

Hi, everyone! Is there anyone here familiar with or using the RTCGAToolbox package? I found it to be very useful when importing, compiling and exporting data from the Firehose repository. However, I am simply unable to export miRNA data. Here is what I'm doing:

> miOV <- getFirehoseData(dataset="OV", runDate = "20160128",  gistic2Date = NULL, clinical = TRUE, miRNAArray = T, forceDownload = T)

And it works fine:

> miOV
OV FirehoseData objectStandard run date: 20160128 
Analysis running date: N/A 
Available data types: 
    clinical: A data frame of phenotype data, dim:  591 x 21 
    miRNAArray: A list of FirehosemRNAArray object(s), length:  1 
To export data, use the 'getData' function.

Now, when I try to export it, it gives me the following message:

> miRNAData <- getData(OV_miRNA, "miRNAArray")

Error in .getListData(getElement(object, type), platform) : argument "platform" is missing, with no default

I checked what the acceptable arguments were, and it describes as:

An index for data types that may come from multiple platforms (such as mRNAArray), for GISTIC data, one of the options: 'AllByGene' or 'ThresholdedByGene'

In this case, I checked the platform for this specific set of data, which was performed on Agilent Human miRNA microarray Rel12.0.

I tried adding "Agilent", "Agilent Human miRNA", and other values, but it didn't work.

Would anybody have any idea on how to solve this issue? Thanks!

R rtcgatoolbox mirna firehose • 375 views
ADD COMMENTlink modified 11 months ago by zx87548.3k • written 11 months ago by dodausp120
2
gravatar for dodausp
11 months ago by
dodausp120
Denmark/Copenhagen/BRIC
dodausp120 wrote:

Case solved! Although it still gives an error message after performing the getData function, it still exports the data.

ADD COMMENTlink written 11 months ago by dodausp120

Case solved!

Could you add more details how this was resolved?

ADD REPLYlink written 11 months ago by zx87548.3k

I just performed the same lines as above. Although the message error was still there, the file was successfully exported to the home directory. So, this should do:

> miOV <- getFirehoseData(dataset="OV", runDate = "20160128",  gistic2Date = NULL, clinical = TRUE, miRNAArray = T, forceDownload = T)
> miRNAData <- getData(OV_miRNA, "miRNAArray")
ADD REPLYlink written 11 months ago by dodausp120
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