User: a.karanikolou

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Posts by a.karanikolou

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Comment: C: affycoretools package, HTA 2.0 annotation query
... Thank you a lot for this. The response from Affy was that and I quote "67528 Probe sets listed: 44699 Coding and 22829 NonCoding". The categories used as controls are sum up to 2,995. The is no clear understanding why Affy is calling at least one probe per probeset an NA type. But we will take your ...
written 3 months ago by a.karanikolou0
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Comment: C: affycoretools package, HTA 2.0 annotation query
... Dear James, thank you for your previous reply. We have used the function getMainProbes using the default as in rma, however instead of the 67,528 main probes that should have been retained, the result was 67,480 main probes. What would cause this difference? Thanks in advance. ...
written 3 months ago by a.karanikolou0
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Comment: C: affycoretools package, HTA 2.0 annotation query
... 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. ...
written 4 months ago by a.karanikolou0
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Comment: C: affycoretools package, HTA 2.0 annotation query
... Thank you for your help. ...
written 4 months ago by a.karanikolou0
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affycoretools package, HTA 2.0 annotation query
... 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(e ...
annotation affy written 4 months ago by a.karanikolou0 • updated 4 months ago by James W. MacDonald51k

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