User: Freudenberg, Johannes NIH/NIEHS [E]

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Posts by Freudenberg, Johannes NIH/NIEHS [E]

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Answer: A: GEO and Limma
... Hi Avoks, > I can hardly figure out how to get from the expression set to the analysis... I can't tell what the problem is but my best guess would be that you're dealing with a list here. Each list element correspond to a different platform. So all you need to do is something like > myGSE ...
written 7.5 years ago by Freudenberg, Johannes NIH/NIEHS [E]150
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Answer: A: [question] integration of microarray data from different sources in limma packag
... Hi Sunjae, > Is there any possibility to combine, normalize and analyze them without problems? I think the order should be "normalize, combine, and analyze (hopefully) without problems." I don't really see a way (nor a good reason) for combining the different platforms first and then doing the ...
written 7.5 years ago by Freudenberg, Johannes NIH/NIEHS [E]150
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Answer: A: annotation package for platform GPL2890
... Based on the file you sent, it looks like the IDs you're trying to match do not correspond to the keys in the table. > head(toTable(r10kcodENTREZID)) probe_id gene_id 1 GE1071 64507 2 GE1072 79245 3 GE1073 50693 4 GE1075 117045 5 GE1076 171150 6 GE1077 81682 Please try ...
written 7.5 years ago by Freudenberg, Johannes NIH/NIEHS [E]150
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Answer: A: annotation package for platform GPL2890
... Dear Jing, I couldn't find any problems with r10kcod.db. Can you please be more specific as to what exactly the trouble is? Best, --Johannes -----Original Message----- From: Jing Huang [mailto:huangji@ohsu.edu] Sent: Tuesday, September 20, 2011 1:00 PM To: bioconductor at r-project.org Subject: ...
written 7.5 years ago by Freudenberg, Johannes NIH/NIEHS [E]150
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Answer: A: Detecting Up-Regulated Genes
... Hi Anirban, A good start would be the limma package. > library(limma) > limmaUsersGuide() Then go to chapter 8.8 "Time Course Experiments" --Johannes -----Original Message----- From: ANIRBAN BHAR [mailto:aec.ani@gmail.com] Sent: Thursday, September 08, 2011 12:07 PM To: bioconductor at r ...
written 7.6 years ago by Freudenberg, Johannes NIH/NIEHS [E]150
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Comment: C: topTable (fit) annotation
... Hi Jing, I'm not quite sure I understand your question. Why can't you use the data for further analysis? Maybe the issue is that getGEO() returns a list? Have you tried something like: > gse16962 <- getGEO("GSE16962") > eset <- gse16962[[1]] > head(fData(eset)) ID ...
written 7.6 years ago by Freudenberg, Johannes NIH/NIEHS [E]150
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Answer: A: GEOquery package
... Hi Jing, The values you show certainly look like they are already on the log- scale. But just to be sure you can quickly check the GEO website: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM424764 About half way down the page it says something like: "Data table header descriptions ID_REF ...
written 7.6 years ago by Freudenberg, Johannes NIH/NIEHS [E]150
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Answer: A: normalization one color microarrays
... Hi Paz, I was able to run the code that you sent me without any trouble. However, here is the output I get: FILTERING BY ControlType FLAG ------------------------------------------------------ PROBES BEFORE FILTERING: 12015 PROBES AFTER ControlType FILTERING: 11259 RAW DATA WITHOUT CONTROLS O ...
written 7.6 years ago by Freudenberg, Johannes NIH/NIEHS [E]150
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Comment: C: normalization one color microarrays
... Can you please be more specific? I'm not really sure what step 14 is. What exactly doesn't work? Please provide an example that doesn't work for you and the kind of error messages it produces. It's also a good idea to provide the output of > sessionInfo() when you post a question like this t ...
written 7.6 years ago by Freudenberg, Johannes NIH/NIEHS [E]150
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Comment: C: normalization one color microarrays
... Hi Paz, I'm not exactly sure what kind of microarrays you are trying to process but I'm guessing you are talking about Agilent 4x44 gene expression arrays. If that is the case, I would recommend to use the Agi4x44Preprocess package. You can download this package here: http://www.bioconductor.org ...
written 7.6 years ago by Freudenberg, Johannes NIH/NIEHS [E]150

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