pData function not found. substitute? "An end to end workflow for differential gene expression using Affymetrix microarrays"
1
1
Entering edit mode
2.5 years ago
RNAseqer ▴ 190

I am currently tinkering with an analysis bioconductor ppackage found here:

"An end to end workflow for differential gene expression using Affymetrix microarrays" https://bioconductor.org/packages/devel/workflows/vignettes/maEndToEnd/inst/doc/MA-Workflow.html

Under section 4.5 you perform the task of running a general linearized model where sva surrogate variables are modeled as a function of your covariates. The following does this by pulling from an expression set object created in the first part of the pipeline:

glm.sv1 <-glm(pData(inpData_sv)[,"sv1"]~pData(inpData_sv)[,"Batch"]+pData(inpData_sv)[,"Sex"])

Unfortunately, I am getting an error telling me:

Error in pData(inpData_sv) : could not find function "pData"

I have tried getting the pData function by downloading ballgown and phylobase, the only two packages where I have seen pData(). Neither of these have seemed to provide me with the pData function required here. I'm pretty new to R, so could anyone recommend a substitute function for this R command?

pvca bioconductor sva pData R • 1.5k views
ADD COMMENT
3
Entering edit mode
2.5 years ago
zx8754 10k

From the linked manual:

The pData function of the Biobase package...

Do you have Biobase package installed/loaded?

ADD COMMENT
0
Entering edit mode

I sure thought I had biobase. I Re-installed it just in case.

Loading the library though...that I forgot.

This seems to have fixed the problem. Thanks!

ADD REPLY

Login before adding your answer.

Traffic: 1449 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6