Question: How to analyze count matrix from Synapse.org
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gravatar for yzfmonster
5 weeks ago by
yzfmonster20
yzfmonster20 wrote:

Hi all,

I downloaded this file from Synapse.org, which is a count matrix for RNAseq data. https://www.synapse.org/#!Synapse:syn5053498

I downloaded it to R, and this file is Formal Class File. I do not know how to proceed with this file to analyze the data.

Any help would be appreciated!

rna-seq data analysis synapse • 168 views
ADD COMMENTlink written 5 weeks ago by yzfmonster20

There is no such thing as a "Formal Class File" in R. I don't want to create an account just to check this file, but it seems a plain text file. How did you load it into R? Depending on the method used, then the resulting object may be of a particular class (instead of being a matrix, for example).

ADD REPLYlink written 5 weeks ago by h.mon10k

Hi Thank you for reply.

I downloaded by first installing their interface package called synapseClient. and logged in by synapseLogin.

library(synapseClient)
synapseLogin('login', 'pw', rememberMe = T)

and I use the code below to get the file "syn5053499"

syn5053499 <- synGet(id='syn5053499')
ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by yzfmonster20
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