User: Jason Hackney

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Jason Hackney160
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Posts by Jason Hackney

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Answer: A: Issues about how to filter and annotate the MoGene-2_0-st and MoEx-1_0-st-v1 arr
... Hi Chao, You can always get the sessionInfo in an R session by running the sessionInfo() command. As for the ReportingTools error, I'm pretty sure that the png's were included in the package. I can see them by running $> unzip -l ReportingTools_2.4.0 The files are just misnamed in your error m ...
written 5.0 years ago by Jason Hackney160
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Comment: C: ReportingTools error message
... An embedded and charset-unspecified text was scrubbed... Name: not available URL: ...
written 5.0 years ago by Jason Hackney160
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Comment: C: ReportingTools error message
... Hi Assa, A couple of questions/comments: 1. How many features pass your p-value cutoff of 0.05? 2. Could you provide your sessionInfo, so I can see what version of ReportingTools you're using? I believe the data.frame in the error message comes from the coercion of your DESeqResults object to a d ...
written 5.0 years ago by Jason Hackney160
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Comment: C: [ReportingTools] and DESeq2 results, publish DESeqDataSet using resultsNames oth
... Hi Dimitra, Gabe is correct that if you want a report that includes all three coefficients in the same table, you'll have to design a function to select results from each coefficient and make a data.frame from them. Unfortunately, I don't have a quick piece of code to drop in. Now for your other p ...
written 5.4 years ago by Jason Hackney160
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Comment: C: [ReportingTools] and DESeq2 results, publish DESeqDataSet using resultsNames oth
... Hi Dimitra, Jim is completely correct about using `coef' to pull out the different terms from your model. I just wanted to add that in addition to the one page-per result workflow he showed, you can call publish multiple times on the same object and same report using the different coefficients, e ...
written 5.4 years ago by Jason Hackney160
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[ReportingTools] HTMLReport of DESeq2 results using Ensembl Gene Ids
... Hi Dimitra, There are a couple of ways to do this using ReportingTools. Probably the easiest way is to write a short function that will collect the annotations of interest from the biomart and pass that function on to the publish call in the .modifyDF parameter. Here's a mock-up that I would use f ...
sequencing annotation convert biomart reportingtools deseq2 written 5.5 years ago by Jason Hackney160 • updated 4.4 years ago by andrew.j.skelton73310
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Comment: C: Question about ReportingTools used with DESeq2
... Hi Amandine, Jim is correct. We were using a deprecated parameter for annotating genes. The current dev version (2.3.3) should no longer throw that warning. Thanks, Jason On Nov 21, 2013, at 8:11 AM, James W. MacDonald wrote: > Hi Amandine, > > This warning just means that the Reportin ...
written 5.6 years ago by Jason Hackney160
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ReportingTools package
... Hi Hena, > I am using the package ReportingTools and would like to know if is it possible to publish t statistics in the report for differential expression analysis using limma? This depends quite a bit on what version of ReportingTools you are using. For the current release version, there are ...
reportingtools written 5.6 years ago by Jason Hackney160 • updated 5.6 years ago by hena ramay10
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Comment: C: ReportingTools - trouble incorporating annotations
... Hi Sam, Sorry for missing so much of the discussion! On Wed, Jun 19, 2013 at 3:17 PM, Sam McInturf wrote: > Still having some troubles : / > > My intention was to load annotation data into a $genes slot for publish() > to pick up by not including the annotations argument in the publ ...
written 6.0 years ago by Jason Hackney160
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Answer: A: ReportingTools: formatting html report
... Hi Abhi, I'm glad that you've gotten RpeortingTools working. Perhaps Josh can discuss a bit how to customize the alignment and spacing of the tables that are produced. I'm much less familiar with the CSS options that exist. For your second question, we can look to the examples in the microarray an ...
written 6.0 years ago by Jason Hackney160

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