User: Ramzi TEMANNI

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Ramzi TEMANNI160
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8 years, 5 months ago
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10 years ago
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Posts by Ramzi TEMANNI

<prev • 15 results • page 1 of 2 • next >
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Answer: A: Basic R question
... Best, Ramzi TEMANNI +31683862423 http://www.linkedin.com/in/ramzitemanni Hi Nathalie, sure you can easily do that by using the dir command: * files.list=dir(path = ".", pattern = "csv") * lest say you have files with extension csv the command dir will store the file names in myfiles then you loo ...
written 8.4 years ago by Ramzi TEMANNI160
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Answer: A: Basic R question
... Hi Nathalie, this code sould give you the expected results: data=read.table("data.csv",header=T) # read data file for (i in unique(data$chrom) ) { write.table(data[which(data$chrom==i),],paste("data",i,".csv",sep=""), row.names=F) # generate 1 file per Chr } Best, Ramzi TEMANNI http://www.link ...
written 8.4 years ago by Ramzi TEMANNI160
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sorting FASTQ file by ID
... Hi everyone, I have paired end data in fastq format where forward and reverse file have different number of reads and are not ordered(based on their id) . I write the following code to mate the reads but seems that *srsort* do not sort id. could anyone tell me what would be the function to use and i ...
process written 8.9 years ago by Ramzi TEMANNI160
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package to handle Infinium iSelect HD Custom Genotyping
... Hi, I have data (txt & idat) of custom iSelect HD custom array and have the bpm(bead pool manifest) file and a csv file and would be intrested in normalizing analyzing. I have 5105 snp on the array but only 148 are of intrest and there's no way to subselect the 148 prior normalization in GenomeS ...
snp normalization crlmm written 9.6 years ago by Ramzi TEMANNI160
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Beadarray data manipulation
... Hello, I have 2 one color Beadarray(HumanRef8 v3) and i'm intrested in comparing diffirentially expressed genes at bead level. Raw file is a 4 column text file Code Grn GrnX GrnY 10008 750 1376.448 8700.565 10008 682 1781.302 12418.69 10008 510 1555.273 6437.563 10008 714 910.3025 1081.659 Ther ...
annotation written 9.7 years ago by Ramzi TEMANNI160 • updated 9.7 years ago by Mike Smith4.0k
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generate a CDF file from Affymetrix ST array 1.1 library
... Hi, I have GeneChip Rate gene 1.1 st array and for some reason cdf library is not available with these array. there's the following file instead *.clf (CEL Layout File): which indicates the location of each probe within the CERevision Date 20090608:L matrix *.pgf (Probe Group File): which indicates ...
cdf probe process written 9.9 years ago by Ramzi TEMANNI160 • updated 9.9 years ago by Benilton Carvalho4.3k
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Comment: C: arrayQualityMetrics Error
... Hi Jim, Thanks for your answer, it's my first experience with Affy data, I used to work with Agilent before. I take a look at the vignette and generated the requested file based on the info about the htmg430pm data : array htmg430pmcdf alpha1 0.05 alpha2 0.065 spk bioB AFFX-r2-Ec-bioB-3_at spk bioC ...
written 9.9 years ago by Ramzi TEMANNI160
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arrayQualityMetrics Error
... Hi, I'm runing some QC analysis with 5 Affy mouse genechip HT430PM I've installed the required libraries(affy, arrayQualityMetrics, htmg430pmcdf) and all dependecies I'm using the following code: fls <- list.files("/", ".*CEL") eset <- justRMA(filenames = fls) aBatch <- ReadAffy(filenames = ...
cdf affy arrayqualitymetrics written 9.9 years ago by Ramzi TEMANNI160 • updated 9.9 years ago by Groot, Philip de630
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Comment: C: ShortRead internal: too many 'snap' entries
... Hi Martin, Thanks for your reply. I've take a look at the file and you are right the problem arise of an abnormal termination of the conversion from scarf to fastq on that file. problem corrected and things are running smooth now. Have a nice day. Regards, Ramzi ------------------------------------- ...
written 9.9 years ago by Ramzi TEMANNI160
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ShortRead internal: too many 'snap' entries
... Hi, I'm using the following function to extract a subselection of reads based on their ID from a FastQ file: extract.reads.fq<-function(dir,fq.file,id.list) { rfq <- readFastq(dir, pattern=fq.file) tmp=extract.id(rfq) sv.reads=rfq[which(id.list%in%tmp)] writeFastq(sv.reads, paste("sv_",fq.file ...
shortread written 9.9 years ago by Ramzi TEMANNI160 • updated 9.9 years ago by Martin Morgan ♦♦ 24k

Latest awards to Ramzi TEMANNI

Popular Question 8.4 years ago, created a question with more than 1,000 views. For sorting FASTQ file by ID
Popular Question 8.4 years ago, created a question with more than 1,000 views. For arrayQualityMetrics Error
Popular Question 8.4 years ago, created a question with more than 1,000 views. For Extract gene name from chromosome position

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