User: Maciej Jończyk

gravatar for Maciej Jończyk
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Posts by Maciej Jończyk

<prev • 71 results • page 1 of 8 • next >
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Loading eSet.r objects from ArrayExpress
... Hi, I have similar problem: > source("E-GEOD-31763.eSet.r") B??d w *error in* source("E-GEOD-31763.eSet.r") : niepoprawny wielobajtowy znak w parserze w linii 11 *invalid multibyte character in parser in line 11* Dodatkowo: By?o 50 lub wi?cej ostrze?e? (u?yj 'warnings()' aby zobaczy? pierwsz ...
written 5.5 years ago by Maciej Jończyk720
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does contamination bother the normalization in transcriptome analysis
... Dear Peter, > > i got 70458 transcripts of one worm by de novo assembly, > but i found 11825 of them are Escherichia contamination. > i think if i donot remove them,it will bother the later analysis, > e.g. > normalization ?? As normalization relays mainly on intensities (except ...
normalization written 5.9 years ago by Maciej Jończyk720
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Comment: C: XML package - 500 internal server error
... It seem that my problem is caused by my faculty network settings. Sorry I solicited you. Best Wishes, thanks for your time ...
written 6.0 years ago by Maciej Jończyk720
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Comment: C: XML package - 500 internal server error
... Sean Davis writes: I've tried to install the packages again. Please find below error messages for GEOquery and ArrayExpress. I've tried to download the XML package source but it failed. In fact I'm able to download empty archive. Hi, Maciej. > > I believe the XML package is available. I ...
written 6.0 years ago by Maciej Jończyk720
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XML package - 500 internal server error
... Hi all, are XML package available? I've tried to install it from varius mirrors and it still fails, giving error '500 Internal Server Error'. I need it to install GEOquery and ArrayExpress. Installation of these packages failed because of XML package instalation failure. In fact I'm not able to ...
geoquery arrayexpress written 6.0 years ago by Maciej Jończyk720 • updated 6.0 years ago by Sean Davis21k
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Answer: A: Limma/Affy - Include expression Intensity in Final 'decideTests' results
... Hi Atul, > > Hi All, > > I am using 'affy' and 'limma' to analyze affymetrix data. > > Simplified code: > > mydata <- ReadAffy() > esetRMA <- rma(mydata) > sampletype <- c('1','1','1','2','2','2','3','3','3','4','4','4') > group <-factor(sampletype) > ...
written 6.0 years ago by Maciej Jończyk720
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Answer: A: Fwd: problem with reading gpr files
... > From: konika chawla > > Subject: [BioC] Fwd: problem with reading gpr files > (Posting it a second time ..) Hi I am new to analyzing gpr files and > I am getting an error in the first stage of reading them. > > > library(limma) myfiles <- dir(pattern=3D"gpr") RG ...
written 6.1 years ago by Maciej Jończyk720
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qRT-PCR - reading tab-delimited file (biol & tech replicates)
... Hi All, I've been asked for analysis of qRT-PCR data. I don't have raw data (from qPCR machine) but excel file (which I planned to transform to tab-delimited text file). I've read manuals for r-packages available, ReadqPCR package seems most promising (taking into consideration data import). There ...
qpcr readqpcr written 6.2 years ago by Maciej Jończyk720
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Answer: A: Query regarding limma
... Hi Roopa, > results <- decideTests(fit2, adjust="fdr", p=0.05) > summary(results) > write.table(results,file="myresults.txt") > > The results table shows ~10,000 genes to be upregulated and ~12,000 > genes > to be down regulated. > > My question is how can I get fold c ...
written 6.2 years ago by Maciej Jończyk720
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Windows or Excel to R txt file
... > i am wondering whether there is a special need to "clean up" txt > files > that were created in windows or Excel before using them in R. > if so, how would you clean them? There are special package "foreign" which allows to read external data (such as xls). As for txt files (tab-deli ...
written 6.3 years ago by Maciej Jończyk720

Latest awards to Maciej Jończyk

Popular Question 5.5 years ago, created a question with more than 1,000 views. For [Mfuzz] Error in cmeans(exprs(eset)
Popular Question 5.5 years ago, created a question with more than 1,000 views. For missing value where TRUE/FALSE needed (metaArray)
Popular Question 5.5 years ago, created a question with more than 1,000 views. For Duplicated Gene IDs - averaging

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