microarray bioinformatic analysis in R

Question

[bioinformatics]

Hi,

I'm trying to perform a microarray differential expression analysis using data downloaded from NCBI.

These are the commands I've done:

files = list.files("/user/GSM4837048_JX65.CEL.gz,GSM4837049_JX66.CEL.gz",full.names = TRUE)
affy.data = ReadAffy(filenames = files)
 eset.mas5 = mas5(affy.data)

However for the last command I get the error message: background correction: mas PM/MM correction : mas expression values: mas background correcting...Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain Clariom_S_Human Library - package clariomshumancdf not installed Bioconductor - clariomshumancdf not available

Do you know how I might download/load the package clariomshumancdf?

Thankyou

Answer 1

[rishav513]

Kindly follow this link :

https://support.bioconductor.org/p/118573/

[bioinformatics]

I have read through the post, do you know how I might use oligo package and PdInfo package to analyse this microarray data? Do the commands I used change? If so, do you know what they should be?

Answer 2

[rishav513]

There are various tutorials available. First of all, do your best from your side.

Kindly look below the tutorial:

https://wiki.bits.vib.be/index.php/Analyze_your_own_microarray_data_in_R/Bioconductor