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pData function not found. substitute? "An end to end workflow for differential gene expression using Affymetrix microarrays"

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
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updated by zx8754 zx8754 • written by RNAseqer RNAseqer

1 answer

From the linked manual:

The pData function of the Biobase package...

Do you have Biobase package installed/loaded?

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written by zx8754 zx8754

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!

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written by RNAseqer RNAseqer

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they all work.

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written by zx8754 zx8754

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