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Is it possible to read in Bluefuse and Agilent files together using read.maimages() function in limma?

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Parisa Razaz ▴ 40

@parisa-razaz-5306

Last seen 9.7 years ago

Hi, Is it possible to read in both Bluefuse and Agilent files together using the read.maimages() function in limma? Thanks, Parisa The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the a...{{dropped:5}}

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ADD COMMENT • link updated 12.0 years ago by Gordon Smyth 50k • written 12.0 years ago by Parisa Razaz ▴ 40

score 0 · Answer 1 · 2012-06-01

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Gordon Smyth 50k

@gordon-smyth

Last seen 4 hours ago

WEHI, Melbourne, Australia

No, it can't combine any two types. Read them in instead using separate calls to read.maimages(). Gordon On Fri, 1 Jun 2012, Parisa Razaz wrote: > Hi, > > Is it possible to read in both Bluefuse and Agilent files together using the read.maimages() function in limma? > > Thanks, > > Parisa ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}

ADD COMMENT • link 12.0 years ago Gordon Smyth 50k

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Hi, Thanks for getting back to me. If I read the two file types in separately, would it be possible to then normalise and analyse the data together (after merging)? I am hoping to follow a protocol similar to that outlined here: http://matt icklab.com/index.php?title=Single_channel_analysis_of_Agilent_microarr ay_data_with_Limma Thanks, Parisa On 1 Jun 2012, at 11:19, Gordon K Smyth wrote: No, it can't combine any two types. Read them in instead using separate calls to read.maimages(). Gordon On Fri, 1 Jun 2012, Parisa Razaz wrote: Hi, Is it possible to read in both Bluefuse and Agilent files together using the read.maimages() function in limma? Thanks, Parisa ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:18}}

ADD REPLY • link 12.0 years ago Parisa Razaz ▴ 40

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Dear Parisa, I've never tried to normalize together intensity data from different image analysis programs. Even if the microarray platforms were the same in both cases, I would view that as a risky procedure. If you were to attempt it, you would need to attend very carefully to batch correction between the platforms as part of the downstream analysis. If you are processing Agilent data, please follow the case study in the limma User's Guide that deals with single-channel Agilent data. It is Section 11.8 titled "Agilent Single-Channel Data: Gene expression in thymus from female Wistar rats". Best wishes Gordon On Fri, 1 Jun 2012, Parisa Razaz wrote: > Hi, > > Thanks for getting back to me. > > If I read the two file types in separately, would it be possible to then > normalise and analyse the data together (after merging)? I am hoping to > follow a protocol similar to that outlined here: > http://matticklab.com/index.php?title=Single_channel_analysis_of_Agi lent_microarray_data_with_Limma > > Thanks, > > Parisa > > > On 1 Jun 2012, at 11:19, Gordon K Smyth wrote: > > No, it can't combine any two types. Read them in instead using separate > calls to read.maimages(). > > Gordon > > On Fri, 1 Jun 2012, Parisa Razaz wrote: > > Hi, > > Is it possible to read in both Bluefuse and Agilent files together using the read.maimages() function in limma? > > Thanks, > Parisa ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}

ADD REPLY • link 12.0 years ago Gordon Smyth 50k