Thank you very much ! indeed without the GSM845651.CEL it works well.
How do you detect the problem ??
Best
Nicolas


2014-02-11 19:56 GMT+01:00 Benilton Carvalho <beniltoncarvalho@gmail.com>:

> Assuming that you were lucky enough to get GSE34243,  try excluding sample
> 16...
>
> In the meantime, will consider how to handle such uncommon samples during
> background correction.
>
> b
> On Feb 11, 2014 4:06 PM, "Nicolas Servant" <nicolas.servant@gmail.com>
> wrote:
>
>> Dear all,
>>
>> I have downloaded "Affymetrix GeneChip Mouse Exon 1.0 ST" microarrays data
>> from GEO and try to process them.
>>
>> > library(oligo)
>> > library(pd.moex.1.0.st.v1)
>> > exonCELs <- list.celfiles(cel_path, full.names=TRUE)
>> > affyExonFS <- read.celfiles(exonCELs, pkgname = "pd.moex.1.0.st.v1")
>> > exonCore <- oligo::rma(affyExonFS, target = "core")
>> > featureData(exonCore) <- getNetAffx(exonCore, "transcript")
>> > normdata <- exprs(exonCore)
>> > head(exprs(exonCore))
>>         GSM845636.CEL GSM845637.CEL GSM845638.CEL GSM845639.CEL
>> GSM845640.CEL
>> 4305140           NaN           NaN           NaN           NaN
>> NaN
>> 4305147           NaN           NaN           NaN           NaN
>> NaN
>> 4305425           NaN           NaN           NaN           NaN
>> NaN
>> 4305730           NaN           NaN           NaN           NaN
>> NaN
>> 4305790           NaN           NaN           NaN           NaN
>> NaN
>> 4305808           NaN           NaN           NaN           NaN
>> NaN
>>         GSM845641.CEL GSM845642.CEL GSM845643.CEL GSM845644.CEL
>> GSM845645.CEL
>> 4305140           NaN           NaN           NaN           NaN
>> NaN
>> 4305147           NaN           NaN           NaN           NaN
>> NaN
>> 4305425           NaN           NaN           NaN           NaN
>> NaN
>> 4305730           NaN           NaN           NaN           NaN
>> NaN
>> 4305790           NaN           NaN           NaN           NaN
>> NaN
>> 4305808           NaN           NaN           NaN           NaN
>> NaN
>>         GSM845646.CEL GSM845647.CEL GSM845648.CEL GSM845649.CEL
>> GSM845650.CEL
>> 4305140           NaN           NaN           NaN           NaN
>> NaN
>> 4305147           NaN           NaN           NaN           NaN
>> NaN
>> 4305425           NaN           NaN           NaN           NaN
>> NaN
>> 4305730           NaN           NaN           NaN           NaN
>> NaN
>> 4305790           NaN           NaN           NaN           NaN
>> NaN
>> 4305808           NaN           NaN           NaN           NaN
>> NaN
>>         GSM845651.CEL GSM845652.CEL
>> 4305140           NaN           NaN
>> 4305147           NaN           NaN
>> 4305425           NaN           NaN
>> 4305730           NaN           NaN
>> 4305790           NaN           NaN
>> 4305808           NaN           NaN
>> > head(exprs(affyExonFS))
>>   GSM845636.CEL GSM845637.CEL GSM845638.CEL GSM845639.CEL GSM845640.CEL
>> 1          6116          8123          5202          6784          5540
>> 2           296           345           324           392           256
>> 3          5899          8030          5123          6721          5574
>> 4           276           262           252           245           163
>> 5           146           181           200           147           172
>> 6            96           118           111           114           116
>>   GSM845641.CEL GSM845642.CEL GSM845643.CEL GSM845644.CEL GSM845645.CEL
>> 1          6535          8560          5268          6154          5402
>> 2           290           419           318           284           378
>> 3          6800          8286          5163          6511          5514
>> 4           332           348           260           234           311
>> 5           155           211           162           158           150
>> 6           120           148           136           153            89
>>   GSM845646.CEL GSM845647.CEL GSM845648.CEL GSM845649.CEL GSM845650.CEL
>> 1          4597          6446          6260          9346          6683
>> 2           312           294           287           445           309
>> 3          4995          5952          6139          8942          6204
>> 4           212           248           301           282           261
>> 5           403           181           196           182           191
>> 6            95            99           127           146           138
>>   GSM845651.CEL GSM845652.CEL
>> 1          5270          8816
>> 2           410           333
>> 3          6239          7955
>> 4           395           330
>> 5           177           175
>> 6            93           116
>>
>>
>> I think that the RMA function returns NaN values. It seems that I have
>> some
>> data before normalization. Why ?? Do you think that it can come from the
>> annotation package ??
>> Many thanks
>> Best
>> Nicolas
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>

	[[alternative HTML version deleted]]

