PFB and Intensities file number of probes (rows) mismatch

[dvirsegal]

I am curious to understand what happens in two cases of mismatch between PFB and a sample’s intensities file:

PFB contains more probes (the name column) than the sample’s intensities file
PFB contains fewer probes (the name column) than the sample’s intensities file

[kaichop]

Only the overlapping probes will be used in CNV calling. Some people are combining multiple types of arrays together with a single PFB file, so this is the first situation that you mentioned. Occasionally, people use PFB file for v1 of an array to analyze v2 or later version of the same array (or used a wrong PFB file with some overlapping markers), which fits the second scenario that you described.

…

On Wed, Oct 19, 2022 at 6:33 AM Dvir Segal ***@***.***> wrote: I am curious to understand what happens in two cases of mismatch between PFB and a sample’s intensities file: PFB contains more probes (the name column) than the sample’s intensities file PFB contains fewer probes (the name column) than the sample’s intensities file — Reply to this email directly, view it on GitHub <#94>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OANP6SG5FQZYUOQWNLWD7FAZANCNFSM6AAAAAARI7EDZE> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[dvirsegal]

Thank you for your answer