User: Mike Walter

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Mike Walter230
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Posts by Mike Walter

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Answer: A: AgiMicroRna problems
... Dear BioC List, I have difficulties in understanding and retracing the results from GO overrepresentation analysis. I used GOTerms to see if there are any GO Terms overrepresented in a list of DE genes with following code: #define gene universe, select only probes with GO annotation and #transfor ...
written 8.6 years ago by Mike Walter230
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Comment: C: Can't normalize 300+ HuGene arrays in xps
... Hi Christian, Changing the name of the file into"dataRMA" didn't help. So I captured the beginning of the error message just after calculation of common mean finished. It says: SysError in : error writing to file F:/Auswertung/GENEPI_combined/dataRMA.root (-1) (No space left on device) So it seem ...
written 8.6 years ago by Mike Walter230
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Comment: C: Can't normalize 300+ HuGene arrays in xps
... Dear Christian, Thanks for your help. To answer your questions first: I normally use RGui and my disk space was ~100Gb. I also tried the add.data=FALSE option, without success. So I did RMA normalization with 6 arrays in RTerm as you proposed. This worked fine. So I just tried to run RMA on all ar ...
written 8.6 years ago by Mike Walter230
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Can't normalize 300+ HuGene arrays in xps
... Hi all, I have a set of 324 HuGene 1.0 arrays I'd like to normalize all in one batch on a "normal" Windows computer. I allready normalized the arrays in two sets of 180 and 144 samples successfully with xps. When I apply the code below to put the samples all together, my R session just crashes. li ...
xps written 8.7 years ago by Mike Walter230 • updated 8.7 years ago by cstrato3.9k
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Comment: C: removal of genes with low expression values
... Hi Jim, >I wonder if some of the things in the mask file don't actually exist on >the chip? If I try this using the Dilution data, there are no problems: > > > rma(Dilution, subset = featureNames(Dilution)[1:250]) >Background correcting >Normalizing >Calculating Expression & ...
written 8.8 years ago by Mike Walter230
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Comment: C: removal of genes with low expression values
... Hi Jim, I thought of two workarounds to mask the S pombe probes with the code attached below. However, in both attempt R crashes, when I call the rma() function either with the NAs introduced in the Affybatch or the subset option. I guess this would also happen, when I use the mask file to generate ...
written 8.8 years ago by Mike Walter230
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Comment: C: removal of genes with low expression values
... Hi Jim, Unfortunately, we did not use the mask file when scanning the chip. So there is not a single NA in the PM values. So I will go back to the dat file and try to generate a new cel file. Thanks a lot and kind regards, Mike -----Urspr?ngliche Nachricht----- Von: "James W. MacDonald" Gesende ...
written 8.8 years ago by Mike Walter230
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Comment: C: removal of genes with low expression values
... Hi there, I have a question on Affymetrix Yeast 2.0 arrays. These arrays contain about 5000 probesets for budding and fission yeast, respectively. We hybridized budding yeast sample and now I'd like to get rid of all the fission yeast probes before normalization. There is a mask file outlining whic ...
written 8.8 years ago by Mike Walter230
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Answer: A: No changes between Groups using GeneST Arrays from Affymetrix
... Hi Benjamin, I don't have an explanation of your problem but some thoughts maybe. I'd agree with you that the bioinformatics is not the problem with your arrays. I'd rather think it is the sample processing part. First of all, maybe there is not much going on in your experiment (at least keep it a ...
written 9.0 years ago by Mike Walter230
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Comment: C: Problems in MAplot for affybatch objects
... Hi all, Thanks for your help. So I will try to get a grip on Sweave and Latex. The alternativ Sweave sounds pretty good, but gives an error message, when I try to source it (error message and sessionInfo below). I will get back to you if I manage to make the pdfs. Kind regards, Mike > source( ...
written 9.0 years ago by Mike Walter230

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