Dear users, I have a question about miRNA differential profiling between two groups. Someone suggested a further filtering of other small RNAs such as mRNA degradation, etc with lengths similar to miRNA after BAM file (which pre-filtering out longer or shorter ones) read-in. I was wondering what consequences would be if I do NOT conduct this process. In this situation, a miRNA count table contains those contaminated non-coding small RNAs and those small RNAs are brought into DE analysis. My intuitive understanding is that it should be fine as long as the miRNA IDs (say, Entrez IDs)are not shared by other small RNAs during alignment or annotation. thanks in advance. sincerely, William Wu [[alternative HTML version deleted]]

Hi - does not sound as a BioC question but I will be happy to answer: miRNA filtering is important because many processed tRNAs, snoRNAs, piRNAs etc are highly similar to known miRNAs. Hence their presence will screw up your counts Kind regards Alessandro ----------------------------------------------------- Alessandro Guffanti - Bioinformatics, Genomnia srl Via Nerviano, 31 - 20020 Lainate, Milano, Italy Ph: +39-0293305.702 Fax: +39-0293305.777 http://www.genomnia.com "If you can dream it, you can do it" (Walt Disney) -----Original Message----- From: "Wu, Huiyun" <william.wu@vanderbilt.edu> To: "bioconductor@r-project.org" <bioconductor@r-project.org> Date: Wed, 16 May 2012 15:52:00 -0500 Subject: [BioC] miRNA and other small RNAs Dear users, I have a question about miRNA differential profiling between two groups. Someone suggested a further filtering of other small RNAs such as mRNA degradation, etc with lengths similar to miRNA after BAM file (which pre-filtering out longer or shorter ones) read-in. I was wondering what consequences would be if I do NOT conduct this process. In this situation, a miRNA count table contains those contaminated non-coding small RNAs and those small RNAs are brought into DE analysis. My intuitive understanding is that it should be fine as long as the miRNA IDs (say, Entrez IDs)are not shared by other small RNAs during alignment or annotation. thanks in advance. sincerely, William Wu [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor [https://stat.ethz.ch/mailman/listinfo/bioconductor] Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [http://news.gmane.org/gmane.science.biology.informatics.conductor] ----------------------------------------------------------- Il Contenuto del presente messaggio potrebbe contenere informazioni confidenziali a favore dei soli destinatari del messaggio stesso. Qualora riceviate per errore questo messaggio siete pregati di cancellarlo dalla memoria del computer e di contattare i numeri sopra indicati. Ogni utilizzo o ritrasmissione dei contenuti del messaggio da parte di soggetti diversi dai destinatari è da considerarsi vietato ed abusivo. The information transmitted is intended only for the per...{{dropped:10}}