Daer all, I need to use a filtering tools for my data, but i dont know if i use my filtering tools after or before normalization, which is better? Best regards, ML -- Mohamed Lajnef INSERM Unit? 955. 40 rue de Mesly. 94000 Cr?teil. Courriel : Mohamed.lajnef at inserm.fr tel. : 01 49 81 31 31 (poste 18470) Sec : 01 49 81 32 90 fax : 01 49 81 30 99

On Mon, Jun 29, 2009 at 11:12 AM, Mohamed Lajnef <mohamed.lajnef@inserm.fr>wrote: > Daer all, > > I need to use a filtering tools for my data, but i dont know if i use my > filtering tools after or before normalization, which is better? > Normally, filtering is applied after normalization, but it will potentially depend on the array type, the array content, and the normalization method you wish to apply. Sean [[alternative HTML version deleted]]

On Mon, Jun 29, 2009 at 11:30 AM, Mohamed Lajnef <mohamed.lajnef@inserm.fr>wrote: > Dearr Sean, > > thank you for you quik answer, i use Illumina file and i have another > question about normalization within arrays, can i use normalizeWithinArrays > (lowess method) from Limma package ? No. NormalizeWithinArrays is for two-color data. You might want to look at using the lumi or beadarray packages, as they are specifically designed to work with Illumina data. Sean > > > Sean Davis a écrit : > > >> >> On Mon, Jun 29, 2009 at 11:12 AM, Mohamed Lajnef < >> Mohamed.lajnef@inserm.fr <mailto:mohamed.lajnef@inserm.fr>> wrote: >> >> Daer all, >> >> I need to use a filtering tools for my data, but i dont know if i >> use my filtering tools after or before normalization, which is better? >> >> >> Normally, filtering is applied after normalization, but it will >> potentially depend on the array type, the array content, and the >> normalization method you wish to apply. >> >> Sean >> >> > > > -- > Mohamed Lajnef > INSERM Unité 955. 40 rue de Mesly. 94000 Créteil. > Courriel : Mohamed.lajnef@inserm.fr tel. : 01 49 81 31 31 (poste 18470) > Sec : 01 49 81 32 90 > fax : 01 49 81 30 99 > [[alternative HTML version deleted]]