Dear Gordon, THANK you so much for answering my question. I will check it out the eset data more detail. Both you and Wolfgang email are really helpful. Many many thanks Jing On 9/12/11 4:19 PM, "Gordon K Smyth" <smyth at="" wehi.edu.au=""> wrote: >Dear Jing and Wolfgang, > >lmFit() allows for NA/NaN/Inf values in the expression object, so simply >having such values in the data isn't the problem. However I agree with >Wolfgang that there is likely to be a serious problem with the expression >object to cause this error to occur. I am guessing that the data is >degenerate in some way. > >Jing, we can't help you with this further given the limited information >you've provided. As Wolfgang says, you need to examine your data more >closely. A first step would be: > > summary(exprs(eset)) > >Best wishes >Gordon > >> Date: Sun, 11 Sep 2011 23:17:22 +0200 >> From: Wolfgang Huber <whuber at="" embl.de=""> >> To: bioconductor at r-project.org >> Subject: Re: [BioC] fit=lmFit limma package >> >> Jing >> >> have a look at the values >> exprs(eset) >> Given the message you see, it appears that these values contain >> NA/NaN/Inf values. In that case, you need to investigate the procedure >> by which you created 'eset' for when & how that happens. >> >> Best wishes >> Wolfgang >> > >> Sep/10/11 2:33 AM, Jing Huang scripsit:: >>> Dear All members, >>> >>> I am trying to analyze GEO data and have used lots of ???limma??? >>>package. Occasionally, I got this R error : >>> >>>> library(limma) >>>> fit=lmFit(eset,design) >>> Error in lm.fit(design, t(M)) : >>> NA/NaN/Inf in foreign function call (arg 4) >>> >>> Everything else seems right. >>> >>> Can somebody help me with this? >>> >>> Many Thanks >>> >>> Jing > > >_____________________________________________________________________ _ >The information in this email is confidential and inten...{{dropped:6}}