Question: Retrieving miRNA data from Firehose by using RTCGAToolbox
1
gravatar for dodausp
5 weeks ago by
dodausp110
Denmark/Copenhagen/BRIC
dodausp110 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 • 130 views
ADD COMMENTlink modified 5 weeks ago by zx87546.2k • written 5 weeks ago by dodausp110
2
gravatar for dodausp
5 weeks ago by
dodausp110
Denmark/Copenhagen/BRIC
dodausp110 wrote:

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

ADD COMMENTlink written 5 weeks ago by dodausp110

Case solved!

Could you add more details how this was resolved?

ADD REPLYlink written 5 weeks ago by zx87546.2k

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 5 weeks ago by dodausp110
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