affy.wave.compute not found

[apastore]

Thanks for this package! Could you tell me how to compute the wave for Oncoscan_CNV and hg38?

Wave re-normalization ... [lski2446:35064] Could not find a Wave data package for [OncoScan_CNV, hg38] in package 'affy.CN.norm.data' ! Please build your own Wave data pack with affy.CN.norm.data::affy.wave.compute() and submit it using the 'renorm.rda' option.

affy.CN.norm.data::affy.wave.compute() Error: 'affy.wave.compute' is not an exported object from 'namespace:affy.CN.norm.data'

[aoumess]

Hi, thanks for testing EaCoN !

Building a wave package for an Affymetrix design is quite a process : it requires you to analyze normal samples (from public datasets found on GEO or ArrayExpress) for the corresponding design, then combine them to build corresponding tracks (using the function depicted in the error message). As I made it for the hg19 build, I can do it for you for hg38, if you want to ?

[apastore]

Thanks! Yes I have seen in the hg19 wave that you made something like that, but I did not find a description how To do it. Also I could not find the wave construction function in the package affy.CN.norm.

IT would be really nice if you could include wave normalization for hg38 (in my case i am interested in ONCOSCAN and ONCOSCOSCAN_CNV Array)

Thanks a lot!! Really appreciate your help! Alessandro

On Jan 17, 2019, at 8:06 AM, Bastien Job [email protected] wrote:

Hi, thanks for testing EaCoN !

Building a wave package for an Affymetrix design is quite a process : it requires you to analyze normal samples (from public datasets found on GEO or ArrayExpress) for the corresponding design, then combine them to build corresponding tracks (using the function depicted in the error message). As I made it for the hg19 build, I can do it for you for hg38, if you want to ?

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[aoumess]

Hi Alessandro,

Just a few words to tell you that I generated hg38 wave tracks for most used Affy designs (CytoScan HD, OncoScan / OncoScan_CNV, and snp6), I'll build and push corresponding updates on Monday ! Regards,

Bastien

[apastore]

Thanks a lot! I will rerun on my data and run some QC! Alessandro

On Jan 25, 2019, at 10:44 AM, Bastien Job [email protected] wrote:

Hi Alessandro,

Just a few words to tell you that I generated hg38 wave tracks for most used Affy designs (CytoScan HD, OncoScan / OncoScan_CNV, and snp6), I'll build and push corresponding updates on Monday ! Regards,

Bastien

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[aoumess]

Hi Alessandro,

OK, I lacked time (and will lack for the next 10 days) to properly insert the code modification to automatically handle the wave correction (ie, without specifiying a specific .rda data pack when running OS.Process), but to spare you some time, I packed a new build of the affy.CN.norm.data package including the new wave data packs) here : affy.CN.data.norm v1.0.3 that you can install manually. As a sidenote, OncoScan arrays usually do not suffer much from wave effect, so adding this normalization step may be non-necessary (but won't affect negatively your results in this case). When I'll be back I'll push a v0.3.5 of EaCoN that will be directly synched with these new data sets. Cheers !

[apastore]

Thank! Much appreciate!

On Jan 30, 2019, at 10:05 AM, Bastien Job [email protected] wrote:

Hi Alessandro,

OK, I lacked time (and will lack for the next 10 days) to properly insert the code modification to automatically handle the wave correction (ie, without specifiying a specific .rda data pack when running OS.Process), but to spare you some time, I packed a new build of the affy.CN.norm.data package including the new wave data packs) here : affy.CN.data.norm v1.0.3 that you can install manually. As a sidenote, OncoScan arrays usually do not suffer much from wave effect, so adding this normalization step may be non-necessary (but won't affect negatively your results in this case). When I'll be back I'll push a v0.3.5 of EaCoN that will be directly synched with these new data sets. Cheers !

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[aoumess]

Errr... @apastore It appears that I did not have a backup of this 1.0.3 package before the shared storage was shut down X°( I'm digging into my hard drive backups but currently can't find it ! Would you still have a copy of it ? or just the hg38 wave packages ? Thanks in advance !

[kunstner]

Same here. Could you please provide a version for hg38? Many thanks!

[kunstner]

Hi @aoumess

would you be able to provide affy.CN.data.norm v1.0.3 again so that EaCoN can be used with GRCh38?

Many thanks!

Best, Axel