User: jayme.rickman

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Posts by jayme.rickman

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Answer: A: Merging files with gene expression data
... I think you likely are looking for the merge function.  Much like Cbind it can bind by columns.  Unlike that it matches them based on matching values (so if in one file the APC gene is like 2 and in the other it is like 400 it can figure that out). The function information is here:https://stat.ethz ...
written 2.6 years ago by jayme.rickman0
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Comment: C: limma decideTests results; how to get/sort most significant Genes?
... in topTable, you can also use the sort.by function so assuming you were writing your code it would be something along the lines of: topTable(fit, number = Inf, sort.by = 'P', ....) ...
written 2.6 years ago by jayme.rickman0
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Comment: C: Affymetrix Rat Transcriptome Array (Clariom D) annotation
...     So, I am the original question asker on the post you referenced.  from having dealt with this (but for the human array) I was able to find a work around. The problem with mine ended up being when you try to annotate the object as an expression set, you can not have repeat names.  As this arra ...
written 2.7 years ago by jayme.rickman0
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Comment: C: Probeset ID's to entrez for Clariom D Human Affy Array
... Thank you for your help any way!  I have also spoken to my internship advisor. Unfortunately she is at a conference this week so her time to help is limited.  If I somehow stumble upon an awnswer I will post it here incase someone else has a problem with these arrays as well ...
written 2.7 years ago by jayme.rickman0
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Comment: C: Probeset ID's to entrez for Clariom D Human Affy Array
... So I am definitely doing something wrong.  I does add the feature set data after the first line of code (where I annotate the 'celfiles.rma' but when I utilize 'getMainProbes' I am returned a list with no features (as in it is saying all of my probes are background probes).   > celfiles.rma &l ...
written 2.7 years ago by jayme.rickman0
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Comment: C: Probeset ID's to entrez for Clariom D Human Affy Array
...     I see.  But RMA via. the oligo package is supposed to remove the background genes (and background noise).   I am not sure if I have potentially done something incorrect up to this point.  as it has been running with out any error.  For reference this is the general workflow so far.  I am admi ...
written 2.7 years ago by jayme.rickman0
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Comment: C: Probeset ID's to entrez for Clariom D Human Affy Array
... Hi James, when I try that method of annotation it just maintains the Affy id's that are provided.  I am trying to get these to entrez id's or gene symbol.  further when I print the head I get 'na' for the additional values > eset <- annotateEset(celfiles.rma, pd.clariom.d.human) > head(fD ...
written 2.7 years ago by jayme.rickman0
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Probeset ID's to entrez for Clariom D Human Affy Array
... I am having trouble figuring out how to transform the probeset ID from the Affy given name to an entrez ID (heck, I would even settle for gene symbols).  My session info is listed at the bottom of this post.  I run into this problem whether utilizing the custom CDF that was given to me by Affymetrix ...
microarray affy written 2.7 years ago by jayme.rickman0 • updated 2.7 years ago by James W. MacDonald50k
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Comment: C: Clariom D Human Microarray CDF file to package
... My apologies, when I have done it with R 3.3.1 that is where I install it.  Just as with R 3.3.0 I generate it and attempt to install it there.  I have posted the full code and than bellow that my general question.  I have included a traceback and the session info.   Creating index idx_pmfsetid on ...
written 2.7 years ago by jayme.rickman0
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Comment: C: Clariom D Human Microarray CDF file to package
... I did upgrade and that seemed to make it work, up until install of the created package, at which point I got an error stating the package was not compatable with R. 3.3.1 (so I tried it all again in R 3.3.0 and got the same error) ...
written 2.7 years ago by jayme.rickman0

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