Question: error after normalizing data
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4 weeks ago by
vasukiperumalla0 wrote:

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘bg.correct’ for signature ‘"HTAFeatureSet", "character"

while performing few operations this error is popping up unable to solve the error im actually working with oligo data and after rma normalization i have used bgcorr = pm(bg.correct(data,method="rma")) this particular code for How to compare raw and background-corrected microarray data how can i solve this problem??

do i need to install an other package ??????

microarray • 75 views
modified 4 weeks ago by James W. MacDonald49k • written 4 weeks ago by vasukiperumalla0
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4 weeks ago by
Guido Hooiveld2.4k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.4k wrote:

Hi, Since you didn't post any code, we have to guess what you did, and what you would like to achieve.... However, based on the very brief error message I assume you are analyzing an HTA array data set. I would suggest to have a look at this thread, in which some code is given that can get you started (RMA normalization is applied). https://support.bioconductor.org/p/89308/

Although you didn't provide a tutorial yourselves (please remove that tag from your post), you can find a tutorial here (for the analysis of a related Affymetrix array type [the Gene ST 1.0]; be sure to change some code accordingly so it matches with the HTA array [e.g. replace pd.hugene.1.0.st.v1 by pd.hta.2.0]). https://f1000research.com/articles/5-1384/v2

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4 weeks ago by
United States
James W. MacDonald49k wrote:

To add to what Guido has already said, if you have already RMA normalized your data, you have by definition already performed background correction (using method = "rma"). In addition, you have summarized all the data and you no longer have probe intensities but instead have probeset intensities. You background correct probes, and then you normalize them, and then you summarize them, which is exactly what happens when you run rma.