Question: Annotation issues with illumina microarray preprocessing with limma
0
gravatar for svlachavas
4.2 years ago by
svlachavas690
Greece/Athens/National Hellenic Research Foundation
svlachavas690 wrote:

Dear ALL,

in addition to one other post i have created regarding illumina microarray preprocessing (https://support.bioconductor.org/p/68196/#68309), i would like to ask you about the important issue of annotation of illumina in limma. As i have preprocessed and analyzed the data with limma, i searched ways to convert the probeIDs to nuIDs in order to have access to "lumiHumanAll.db", because as it mentions "
lumiHumanAll.db is using or is likely to need access to special nuID identifiers.  Users can learn about these identifiers from vignette documentation provided with the lumi package". As the function addNuID2lumi() is only working with lumi batch object, i also search the library lumiHumanIDMapping, but i couldnt find a way to convert the illumina probeIDs, in order to use the lumiHumanAll.db to get gene symbols and other annotation forms. Any ideas or proposals ?. I also tried to use the illumina probeIDs with the function select() but it didnt worked either.

 

ADD COMMENTlink modified 4.2 years ago by Gordon Smyth38k • written 4.2 years ago by svlachavas690
Answer: Annotation issues with illumina microarray preprocessing with limma
1
gravatar for Gordon Smyth
4.2 years ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k wrote:

Just use illuminaHumanv4.db instead. Then there is no need to convert probe IDs.

Or else one can alternatively download the HumanHT-12 V4 manifest file from the Illumina website.

ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by Gordon Smyth38k

Dear Mr. Gordon Smyth,

thank you for your answer !! i thought from the vignette of lumi and other tutorials about illumina analysis (thttps://github.com/csgillespie/illumina-analysis) that due to the inconsistency of annotations between different illumina platforms and other reasons, it is essential to use convert probeIDs to nuIDs(nucleotide universal identifier) and then use the latter to reclame more consistent annotation forms !!

ADD REPLYlink written 4.2 years ago by svlachavas690
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