lumi batch from genomestudio
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kripa raman ▴ 10
@kripa-raman-4554
Last seen 9.5 years ago
Hi everyone! I've just obtained data from illumina HT12 chips and have taken a preliminary look at the data in genomestudio. I'd like to do further analysis in R but I'm having trouble creating the batch file. I've exported the Group_Probe_Profile.txt sheet but when using this I get errors regarding lack of nuID and such. Does anyone have familiarity with doing this; are there other files I'm missing? Some guidance would be greatly appreciated! Thanks, Kripa [[alternative HTML version deleted]]
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Pan Du ▴ 80
@pan-du-4535
Last seen 9.1 years ago
United States
I remember this has been replied yesterday. First, we recommend using "Sample Probe Profile.txt" instead of "Group Probe Profile.txt". "Group Probe Profile.txt" may still work depending on how the group is defined. To avoid trouble, just use "Sample Probe Profile.txt". As for nuID conversion, there are two choices: 1. Set the "convertNuID" parameter as FALSE. In this case, no nuID conversion will be performed. 2. Provide the id mapping package for nuID conversion. For example, if you are using human chips, then set "lib.mapping=lumiHumanIDMapping". BTW, when you report problem, please always attach the sessionInfo() and error message. Pan Date: Tue, 22 Mar 2011 17:13:16 -0400 From: kripa raman <kripa.raman7@gmail.com> To: bioconductor@r-project.org Subject: [BioC] lumi batch from genomestudio Message-ID: <aanlktinspoy=nnvcou6m7of+ t8hfpespz8fz="1DUcHoS@mail.gmail.com"> Content-Type: text/plain Hi everyone! I've just obtained data from illumina HT12 chips and have taken a preliminary look at the data in genomestudio. I'd like to do further analysis in R but I'm having trouble creating the batch file. I've exported the Group_Probe_Profile.txt sheet but when using this I get errors regarding lack of nuID and such. Does anyone have familiarity with doing this; are there other files I'm missing? Some guidance would be greatly appreciated! Thanks, Kripa [[alternative HTML version deleted]]
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