Hi, everybody, Do you agree amplification will delivery bias to RNA-seq

[seattle]

I am currently working with Affymetrix platform. We are evaluating the reproducibility of microarray experiments, finished pilot, training and test studies, with large cohort of samples. It seems to me that microarray technology requires high quality RNA, and RNA amplification, which always delivery bias.

On the other hand, I am very interested to receive quick messages from SEQanswers: whether RNA-seq technology provided by next generation sequencing platforms also demands high quality RNA together with RNA amplification. It could delivery some question to this platform.

What do you think?
Best wishes,
Xun

[ECO]

This would probably be of interest to you when deciding between arrays and sequencing.

http://www.nature.com/news/2010/100518/full/news.2010.248.html

[steven]

This would probably be of interest to you when deciding between arrays and sequencing.

http://www.nature.com/news/2010/1005....2010.248.html

There is written:

Of the transcripts that weren't associated with known genes, most were either very short transcripts or found at very low levels — both signs of simple background 'noise' in transcription. So these transcripts may have no function at all, van Bakel says.

I strongly disagree with this "reasoning".

[seattle]

This site is useful as well for a collection of library protocols from Illumina: http://keck.med.yale.edu/microarrays...protocols.html
It gives pdf library protocols for the following:
Preparing Samples for Whole Transcriptome Profiling

Many thanks to ECO for creating and maintaining the forum. I do appreciate your attached link, and read the paper with great interest.

Illumina RNA-seq requires RNA with RIN value higher than 8. It seems to me that, to perform RNA-seq, it is doable to use samples from Clontech. But it is really challenging to apply this platform to identify predictors using real clinical samples, like tumor biopsy.