[BioC] fit=lmFit limma package

Jing Huang huangji at ohsu.edu
Tue Sep 13 01:24:22 CEST 2011

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


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
>> 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}}

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