[aroma.affymetrix] FIRMA and Gene 1.0 ST

Hi, Got a quick question. Can the FIRMA code for exon array analysis page be applied to Gene 1.0 ST arrays? Thanks! Yu Chuan -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3

[aroma.affymetrix] Re: exon array analysis errors

Hi Elizabeth, Thanks for your comments. They are very helpful! Best, Yu Chuan On Dec 1, 9:39 am, Elizabeth Purdom wrote: > > Also, what does it mean if the boxplot for a chip's exon-level NUSE > > suggests that this chip maybe an outlier (i.e. the median is higher > > th

[aroma.affymetrix] Re: exon array analysis errors

0 0 $`20091119_UHR_Exon3`$n [1] 18705 $`20091119_UHR_Exon3`$conf [1] 0 0 $`20091119_UHR_Exon3`$out numeric(0) attr(,"type") [1] "NUSE" On Nov 30, 1:28 am, Mark Robinson wrote: > Hi Yu Chuan. > > I'm still mystified by this.  Can you check that the PLM was   > suc

[aroma.affymetrix] Re: exon array analysis errors

18705 $`20091119_UHR_Exon3`$conf [1] 0 0 $`20091119_UHR_Exon3`$out numeric(0) attr(,"type") [1] "NUSE" On Nov 24, 9:32 am, Yu Chuan wrote: > Hi Mark, > > Thanks for your prompt reply. Below is my complete R code together > with error information. I tried what you s

[aroma.affymetrix] Re: exon array analysis errors

ity across chips, while gene-level NUSE boxplots don't. And RLE boxplots don't show much heterogeneity either at the exon-level or gene-level. Could someone give me an idea about why this is the case, and whether I should define an outlier based on the gene-level or exon- level NUSE/RL

[aroma.affymetrix] exon array analysis errors

Any idea about how to fix this? Thanks! Yu Chuan -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are

[aroma.affymetrix] Re: selection of "good" probes in exon CDF's

Hi folks, I have a question related to this topic. I want to generate gene-level expression values using the 3' end probes or 5' end probes only. Looks like creating a custom CDF file containing only the probes I want is the only way for that. Is it correct? Thanks

[aroma.affymetrix] Re: Questions about annotations

Hi Mark, Thanks a lot!! Very useful. I think I know what to do now. Best, Yu Chuan On Nov 6, 4:14 am, Mark Robinson wrote: > Hi Yu Chuan. > > Some comments below. > > On 3-Nov-09, at 12:36 PM, Yu Chuan wrote: > > > Hi all, > > > Follow up the below discussi

[aroma.affymetrix] Re: Questions about annotations

proach to get chromosome locations using what I already have, and wonder if anyone has any suggestion? Thanks! Yu Chuan Hi Shuying, So for your main question -- how to get a gene name for a transcript cluster id -- you will probably need to use the Affymetrix annotation for this, regardless of

[aroma.affymetrix] GCRma bg correction for exon 1.0st

Hi, I followed your human exon array analysis page, but used gcrma for background correction. http://groups.google.com/group/aroma-affymetrix/web/human-exon-array-analysis?hl=en However, I got errors shown below. Also, can I correct for probe sequence effect, in addition to GC content? > bc <-

[aroma.affymetrix] Affymetrix Exon Array 1.0ST CDF file

Hi, I am going to start to analyze some Affy exon arrays. I just checked the customized CDF file page and found that the latest ones are developed in Nov. 2007. Is there any more updated versions since then? Thanks! Yu Chuan --~--~-~--~~~---~--~~ When reporting