User: amalbouzid.ing

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Posts by amalbouzid.ing

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Comment: C: How to use cn.mops to detect CNVs from Targeted DNA Sequencing data?
... Dear Günter,  Many thanks for your reply.  I will take that into account! Best, Amal ...
written 3 months ago by amalbouzid.ing0
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Comment: C: How to use cn.mops to detect CNVs from Targeted DNA Sequencing data?
... Please,  there is someone who can answer me for my previous comment??! ...
written 3 months ago by amalbouzid.ing0
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Comment: C: How to use cn.mops to detect CNVs from Targeted DNA Sequencing data?
... Dear  Günter Thanks a lot for all your suggestions that helped me cope! Just to remember, I'm working with targeted sequencing on two samples, one case and one control. I tried with your two previous proposals: 1/The first one:To generate the read counts from BAM Files comparing to whole genome use ...
written 3 months ago by amalbouzid.ing0
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Comment: C: How to use cn.mops to detect CNVs from Targeted DNA Sequencing data?
... Hi Günter,  Thanks for your suggestion! I tried but I think that I make a mistake somewhere?! BAMFiles <- list.files(pattern=".bam$") refSeqName=c(paste0("chr",1:22),"chrX","chrY") DataRanges.smallWL <- getReadCountsFromBAM(BAMFiles, sampleNames=paste("Sample",1:3), refSeqName= refSeqName ...
written 4 months ago by amalbouzid.ing0
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Comment: C: Gene set Testing with Limma for Agilent IDs probes?
... Great! Thanks James. Certainly that always there will be an interest! ...
written 4 months ago by amalbouzid.ing0
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Comment: C: Gene set Testing with Limma for Agilent IDs probes?
... Hello James, Thanks for your quick reply. So afterwards, it will be interesting to focus only on probes mapped to Enter Gene IDs without seeking explanations           of non-mapping for the others!? Thanks, Best,   ...
written 4 months ago by amalbouzid.ing0
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Answer: A: Gene set Testing with Limma for Agilent IDs probes?
... Dear James, Many thanks for your comments and explanation! It really helped me. Absolutely, I'm using the Agilent-026652 arrays. I write to you a bit of my Sherlock Holmes for that step! I added to your code: Considering that  "my probes" is a data farme of my resulted significant probes: > ...
written 4 months ago by amalbouzid.ing0
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Comment: C: LIMMA and Agilent single color
... Dear Gordon, Thanks for your reply and your consideration. I've already posted my question to Bioconductor!  Looking forward to your help :) Thanks, Best regards, ...
written 4 months ago by amalbouzid.ing0
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Gene set Testing with Limma for Agilent IDs probes?
... Hi all, I'm studying Agilent Human Gene Expression one color microarray using Limma. It results significant probes with the topTable function but then I didn't succed to do the conversion of my identifiers with "ids2indices" function? nor later the gene set testing? Please, find below my code, I'm ...
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Answer: A: LIMMA and Agilent single color
... Hi, I'm studying Agilent Human Gene Expression one color microarray using Limma. It results significants probesets with topTable function but then I didn't succed to do the conversion of my probenames with "ids2indices" function? nor the annotation of my genes? Please, there is someone who can hel ...
written 4 months ago by amalbouzid.ing0

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