User: Francois Pepin

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Francois Pepin1.3k
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Posts by Francois Pepin

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agilent reading array data.
... Hi, it's difficult to say for sure without any additional details. One possibility is some strange R configuration, but we can't tell without the information from sessionInfo(). My guess that one of your file is likely corrupt. It is the same size as the others? Can you read your data if you skip ...
written 7.9 years ago by Francois Pepin1.3k
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Comment: C: 转发: Statistical approach to compare differentiall expressed gene lists
... Dear Qinghua, I am not sure if I would call those differences "very impressive". As your samples have different numbers of X and Y chromosomes, I would definitely expect many of them to be differentially expressed. After all, no genes on Y should be expressed on any of the females, right? The fact ...
written 7.9 years ago by Francois Pepin1.3k
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Comment: C: Patent issues of classification algorithms
... Dear Qinghua, I don't think you should concern yourself too much with patents on most classification methods. Yes, there might be lots of SVM patents in a biomedical field, but the basic method for SVM is not patented and the same is true for almost all other methods. Unless something malicious w ...
written 7.9 years ago by Francois Pepin1.3k
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Comment: C: Agi4x44PreProcess
... Hi Neel, you want to have "targets=targets)" at the end of your call to filter.probes. Otherwise it thinks that targets is the value for for the limSAT argument. If you're not going to follow the order of arguments, you should make sure to name every argument in the function. Francois On 12/09/2 ...
written 7.9 years ago by Francois Pepin1.3k
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Agi4x44PreProcess
... (Apologies, I had originally put BioC in bcc instead of cc, whoever is moderating the list should feel free to delete the original) Dear Hemang, Please use the bioconductor mailing list. This will allow other people to help you in addition to ensuring that this e-mail will be archived and searchab ...
convert geoquery agi4x44preprocess written 8.0 years ago by Francois Pepin1.3k • updated 7.9 years ago by Neel Aluru440
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Answer: A: Agi4x44PreProcess
... Dear Hemang, Please use the bioconductor mailing list. This will allow other people to help you in addition to ensuring that this e-mail will be archived and searchable for other people who might have the same issue. While I have commented on the usage of Agi4x44PreProcess and tried to help people ...
written 8.0 years ago by Francois Pepin1.3k
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Answer: A: R: Can an R script be run through a cron job ?
... Hi Maura, your attachment was scrubbed by the list software, it wasn't overlooked. You would be better to have the relevant parts in your e-mail instead. Kasper is referring to the fact that you are sending a different query for each miRNA. Grouping everything together such that you only have a si ...
written 8.0 years ago by Francois Pepin1.3k
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Answer: A: Agilent Array Analysis Question
... Hi Sunny, To answer the questions in reverse order: 3- Yes, Limma is a good choice for it. The user's guide is long but full of extremely useful information. Going through the relevant sections is strongly recommended. 2- Agi4x44PreProcess works well if you have human or mouse 4x44 whole genome ar ...
written 8.0 years ago by Francois Pepin1.3k
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Answer: A: Agi4x44PreProcess - Replicated genes
... Hi Neel, There are a couple of issues here, that I can see. One is that you are not using the proper annotation packages. org.Dr.eg.db is an organism package and would not contain the probe information that would be expected by the functions you are calling. You will have to use the annotation pac ...
written 8.0 years ago by Francois Pepin1.3k
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Comment: C: Agilent zebrafish4x44 database
... Your original code had CV.rep.probes(aa,"zebrafish.db0 ",... I'm assuming this was just a typo in recopying the code, as it wouldn't work if you had the space after the 0. By sessionInfo(), I meant the output of the sessionInfo() function. What you just posted is different than before. You have a ...
written 8.0 years ago by Francois Pepin1.3k

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Centurion 7.9 years ago, created 100 posts.

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