Question: affycoretools package, HTA 2.0 annotation query
0
gravatar for a.karanikolou
4 weeks ago by
a.karanikolou0 wrote:

Hi all, I have recently run the HTA 2.0 annotation using the two packages affycoretools and hta20transcriptcluster.db as outlined in the post https://support.bioconductor.org/p/89308/. However, I have run into an error after running the rma() as follows:

> exprs_mainProbes<-getMainProbes(exprsgs, pd.hta.2.0)
Error in switch(level, core = dbGetQuery(con, paste("select distinct core_mps.transcript_cluster_id, type from featureSet inner join core_mps",  : EXPR must be a length 1 vector

Could you shed light into this problem? Thanks in advance.

annotation affy • 80 views
ADD COMMENTlink modified 4 weeks ago by James W. MacDonald50k • written 4 weeks ago by a.karanikolou0
Answer: affycoretools package, HTA 2.0 annotation query
0
gravatar for James W. MacDonald
4 weeks ago by
United States
James W. MacDonald50k wrote:

You need to become familiar with the help system, and to check there to ensure you are doing things correctly. From ?getMainProbes, we have:

Usage:

     getMainProbes(input, level = "core")

Arguments:

   input: Either a character string (e.g., "pd.hugene.1.0.st.v1") or a
          FeatureSet object.

   level: The summarization level used when calling rma.


And nowhere in the help page does it say that the second argument should be a pdInfoPackage.

ADD COMMENTlink written 4 weeks ago by James W. MacDonald50k

Thank you for your help.

ADD REPLYlink written 4 weeks ago by a.karanikolou0

Is it mandatory to include "level = "core"" in the "getMainProbes(input, level = "core")?

In the "help" menu, the argument "level" refers to "the summarization level used when calling rma". I'm not sure I understand it well on how to apply this argument in getMainProbes.

ADD REPLYlink written 4 weeks ago by a.karanikolou0

If a function has a default, then by definition it isn't necessary to supply a value for that argument. But perhaps you are actually asking what value you should use? Again, the answer to your question can be found by reading the help page, this time for rma:

Description:

     Robust Multichip Average preprocessing methodology. This strategy
     allows background subtraction, quantile normalization and
     summarization (via median-polish).

Usage:

     ## S4 method for signature 'ExonFeatureSet'
     rma(object, background=TRUE, normalize=TRUE, subset=NULL, target="core")
       ## S4 method for signature 'HTAFeatureSet'
     rma(object, background=TRUE, normalize=TRUE, subset=NULL, target="core")

If you didn't specify a target argument for rma, then you by definition used the default, which matches the default for getMainProbes.

ADD REPLYlink written 4 weeks ago by James W. MacDonald50k
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