other.columns = 'gIsWellAboveBG' is not being added to the object

Question

[Fate]

Hey all, Im using Agilent-015058 O. sativa (Rice) Oligo Microarray 4x44K microarray .gpr files. so following the workflow of limma vignette I used the code:

data = read.maimages(targets,source="genepix",green.only = TRUE, other.columns = 'gIsWellAboveBG')

But later for filtering the normalized and background corrected data for probes without expression, I don't find other column via this code

bc_norm_data$other$gIsWellAboveBG

can someone help me how can I add this column? same problem with ControlType for removing control probes via:

data$genes$ControlType==1L

thanks!

Answer 1

[Kevin Blighe]

Hello and good evening,

There is a discrepancy here: you imply that you have Agilent data, but you also mention GPR files, which are from GenePix. Please confirm if you have GenePix or Agilent data?

If you have GenePix data, then gIsWellAboveBG will not be present, and green.only does not apply.

If you genuinely have Agilent data, which should have the extension TXT, then you need to review the value of the source parameter. It needs to be, for example, agilent or agilent.medium

Please see: https://www.rdocumentation.org/packages/limma/versions/3.28.14/topics/read.maimages

Please also see my previous answer: How to process (seems) Agilent microarrry data?

Kind regards,

Kevin

[Fate]

Hello Kevin,

thank you for your kind answer. I am working on this accession GSE58132. so the platform is Agilent-015058 O. sativa (Rice) Oligo Microarray 4x44K (Feature Number version), but the scanner was Axon thus the resulting files have .gpr extension. If the green.only does is not appliable, how can I specify that my data is single-color? Do you happen to know if there are any resources for analyzing .gpr data that I can reffer to?

Regards, Fate