User: amalbouzid.ing

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Posts by amalbouzid.ing

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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 15 hours 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 ...
limma annotation gene set testing agilent microarrays written 15 hours ago by amalbouzid.ing0 • updated 8 hours ago by James W. MacDonald41k
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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 3 days ago by amalbouzid.ing0
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Comment: C: How to use cn.mops to detect CNVs from Targeted DNA Sequencing data?
... Thank you Günter for your reply, but I do not have a list of targeted regions provided as BED file, how can I retrieve it?? Thanks, Best Regards   ...
written 7 days ago by amalbouzid.ing0
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How to use cn.mops to detect CNVs from Targeted DNA Sequencing data?
... Hi, I'm using cn.mops to detect CNVs from Targeted DNA Sequencing data by "TruSight One Sequencing Panel from Illumina" investigated for one patient and one control samples, on an Illumina MiSeq sequencer with 150 bp paired-end run. By running the algorithm with the referencecn.mops function, it re ...
cnv cn.mops targeted sequencing written 9 days ago by amalbouzid.ing0 • updated 9 days ago by Günter Klambauer240
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Quality Assessment of one color Agilent arrays?
... Dear Bioconductor, I have an expression array dataset done with Agilent one color array, and I wanted to do QC using arrayQualityMetrics. I read in the raw Agilent data using limma and background correct and normalization was done according to limma User's guide. This works fine and I got an EList ...

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