Dear Hasuan-Yu Lin,

Although this is an old version and is recommendable to update, your 
problem with R-2.15.1 is described (and solved) here:

https://stat.ethz.ch/pipermail/bioconductor/2014-April/059098.html

The error you get with the release version (3.1.0) has to do with some 
updates and restructuring of the package.  As the error message 
indicates, many functions were deprecated and replaced for new functions 
(in your case, use DEXSeqDataSetFromHTSeq instead of read.HTSeqCounts).  
You will find more details in the new vignette.

Best regards,
Alejandro

> Hi,
>
> I have some question about DEXseq, DESeq, and pasilla!
>
> In the 2013/12/03，I install DEXseq, DESeq, and pasilla in the R-2.15.2, and run the test script, like attached file, fly.R. I have take the right output file (flyRes.txt).
>
> In today (20140515), I re-install R-2.15.2 and DEXseq, DESeq, and pasilla in the same Linux server (Ubuntu 10.04), and run fly.R, but get an error, like file, Error_for_20140515_R-2.15.2.txt, I don't know what happen, and I don't know how to remove this error.
>
> Can you help to remove this error. please!
>
> If I try to install R-3.1.0, this is last version for now, and install DEXseq, DESeq, and pasilla, and run fly.R, but get another error, like file, Error_for_20140515_R-3.1.0. For this error, how to remove it?
>
>
> Thank's for your help!!
>
>
> =====================================
> Hsuan-Yu Lin
> Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, NHRI.
> 35, Keyan Road, Zhunan Town, Miaoli County 35053, Taiwan, ROC
> E-mail：kor@nhri.org.tw
> TEL：(886)-37-246166  ext. 36187
> FAX：(886)-37-586467
>
>
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