Re: [base] Lowess normalisation - Block parameter
Great using 1 worked! Thanks From: Nicklas Nordborg To: BASE ML Sent: Sunday, 8 February, 2009 22:58:08 Subject: Re: [base] Lowess normalisation - Block parameter Louise Donnison wrote: > Hi > I have been trying to normalise with block size 48 using the Lowess > normalization plugin. It does not appear to work for me. > It gives the same result as if I use block size 0. If your array has 48 block on it this is the expected behavior. The parameter tells the plug-in the number of blocks to use per group. If you want to normalize each block individually the value should be '1'. /Nicklas -- Create and Deploy Rich Internet Apps outside the browser with Adobe(R)AIR(TM) software. With Adobe AIR, Ajax developers can use existing skills and code to build responsive, highly engaging applications that combine the power of local resources and data with the reach of the web. Download the Adobe AIR SDK and Ajax docs to start building applications today-http://p.sf.net/sfu/adobe-com ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net -- Create and Deploy Rich Internet Apps outside the browser with Adobe(R)AIR(TM) software. With Adobe AIR, Ajax developers can use existing skills and code to build responsive, highly engaging applications that combine the power of local resources and data with the reach of the web. Download the Adobe AIR SDK and Ajax docs to start building applications today-http://p.sf.net/sfu/adobe-com___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
Re: [base] Lowess normalisation - Block parameter
Louise Donnison wrote: > Hi > I have been trying to normalise with block size 48 using the Lowess > normalization plugin. It does not appear to work for me. > It gives the same result as if I use block size 0. If your array has 48 block on it this is the expected behavior. The parameter tells the plug-in the number of blocks to use per group. If you want to normalize each block individually the value should be '1'. /Nicklas -- Create and Deploy Rich Internet Apps outside the browser with Adobe(R)AIR(TM) software. With Adobe AIR, Ajax developers can use existing skills and code to build responsive, highly engaging applications that combine the power of local resources and data with the reach of the web. Download the Adobe AIR SDK and Ajax docs to start building applications today-http://p.sf.net/sfu/adobe-com ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] Lowess normalisation - Block parameter
Hi
I have been trying to normalise with block size 48 using the Lowess
normalization plugin. It does not appear to work for me.
It gives the same result as if I use block size 0.
I have been looking at LowessNormalisation code.
The spot spot data is ofsize 17328 split over 48 blocks.
When the code executes here the resulting toNormalise is still of size
17328, I was expecting it to be of size 361 ?
while (toIndex < dataSize && data.get(toIndex).block <= toBlock)
{
++toIndex;
}
if (toIndex > fromIndex)
{
List toNormalize = data.subList(fromIndex, toIndex);
Is there something that I am doing wrong?
regards
Louise
The code version is BASE 2.9 using LowessNormalisation code of
@version 2.0 @base.modified $Date: 2008-09-11 22:06:36 +0200 (Thu, 11
Sep 2008) $
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build responsive, highly engaging applications that combine the power of local
resources and data with the reach of the web. Download the Adobe AIR SDK and
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Re: [base] lowess normalisation
The problem is now being fixed, http://base.thep.lu.se/ticket/1077. Unfortunately this problem affects all versions of BASE2 and everyone are recommended to upgrade to the future 2.7.2 (or later). The problem is localized and 2.7.2 will be released later today or at latest tomorrow. More details on the issue will follow in the announcement of the new release. Cheers, Jari Bob MacCallum wrote: > Has anyone had problems with the Lowess analysis plugin? > > To me it looks like it is overcorrecting. Where a M/A plot > is largely below the zero line before normalisation, it ends > up largely above it afterwards. > > I'm using default values (including 0 for block group size). > Default values were always fine in BASE1. > > You can look for yourself with the guest login at > http://fungen.vectorbase.org/base2 > > Experiment "Male vs. female (Koutsos et al., 2007)" is a good > small example. > > I don't see a recent ticket on this (I have not upgraded in > a few months). > > cheers, > Bob. > > - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
Re: [base] lowess normalisation
Thanks very much Jari. Sorry I didn't have time to look deeper and figure out what was wrong. As you'll see in a few weeks we have a big project nearing release. cheers, Bob. Jari Häkkinen writes: > Hi Bob, > > We are looking into the issue. It looks like the BASE2 version of lowess > is flawed. We are testing and reading publications to make sure that we > make a proper fix. We already have a fix for the problem but want to > make sure that we don't create new bugs. We plan to release a 2.7.2 ASAP > with the fix. > > Thank you for reporting this issue to us. > > > Jari > > > Bob MacCallum wrote: > > I've done some more tests on the lowess problem. > > > > Please refer from now on to our development server: > > > > http://base.vectorbase.org:8080/base2dev/ > > Experiment: "Male vs. female (Koutsos et al., 2007)" > > > > I ran the base1 lowess plugin and got a very different result compared to > > the > > base2 plugin. The base1 plugin results look correct to me. The base2 > > correction factor plots do not look at all right to me. > > > > Can anyone hazard a guess as to if this is a bug or are the default > > parameters > > not suitable for my data? > > > > Due to time pressures I think I'm going to have to switch all our analysis > > over to use the base1 plugin. > > > > many thanks, > > Bob. > > > > Bob MacCallum writes: > > > > > > Has anyone had problems with the Lowess analysis plugin? > > > > > > To me it looks like it is overcorrecting. Where a M/A plot > > > is largely below the zero line before normalisation, it ends > > > up largely above it afterwards. > > > > > > I'm using default values (including 0 for block group size). > > > Default values were always fine in BASE1. > > > > > > You can look for yourself with the guest login at > > > http://fungen.vectorbase.org/base2 > > > > > > Experiment "Male vs. female (Koutsos et al., 2007)" is a good > > > small example. > > > > > > I don't see a recent ticket on this (I have not upgraded in > > > a few months). > > > > > > cheers, > > > Bob. > > > > > > > > > -- > > > Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | > > > Division of Cell and Molecular Biology | Imperial College London | > > > Phone +442075941945 | Email [EMAIL PROTECTED] > > > > > > > > - > > > Check out the new SourceForge.net Marketplace. > > > It's the best place to buy or sell services for > > > just about anything Open Source. > > > http://sourceforge.net/services/buy/index.php > > > ___ > > > The BASE general discussion mailing list > > > basedb-users@lists.sourceforge.net > > > unsubscribe: send a mail with subject "unsubscribe" to > > > [EMAIL PROTECTED] > > > > - > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://sourceforge.net/services/buy/index.php > ___ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED] - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
Re: [base] lowess normalisation
Hi Bob, We are looking into the issue. It looks like the BASE2 version of lowess is flawed. We are testing and reading publications to make sure that we make a proper fix. We already have a fix for the problem but want to make sure that we don't create new bugs. We plan to release a 2.7.2 ASAP with the fix. Thank you for reporting this issue to us. Jari Bob MacCallum wrote: > I've done some more tests on the lowess problem. > > Please refer from now on to our development server: > > http://base.vectorbase.org:8080/base2dev/ > Experiment: "Male vs. female (Koutsos et al., 2007)" > > I ran the base1 lowess plugin and got a very different result compared to the > base2 plugin. The base1 plugin results look correct to me. The base2 > correction factor plots do not look at all right to me. > > Can anyone hazard a guess as to if this is a bug or are the default parameters > not suitable for my data? > > Due to time pressures I think I'm going to have to switch all our analysis > over to use the base1 plugin. > > many thanks, > Bob. > > Bob MacCallum writes: > > > > Has anyone had problems with the Lowess analysis plugin? > > > > To me it looks like it is overcorrecting. Where a M/A plot > > is largely below the zero line before normalisation, it ends > > up largely above it afterwards. > > > > I'm using default values (including 0 for block group size). > > Default values were always fine in BASE1. > > > > You can look for yourself with the guest login at > > http://fungen.vectorbase.org/base2 > > > > Experiment "Male vs. female (Koutsos et al., 2007)" is a good > > small example. > > > > I don't see a recent ticket on this (I have not upgraded in > > a few months). > > > > cheers, > > Bob. > > > > > > -- > > Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | > > Division of Cell and Molecular Biology | Imperial College London | > > Phone +442075941945 | Email [EMAIL PROTECTED] > > > > - > > Check out the new SourceForge.net Marketplace. > > It's the best place to buy or sell services for > > just about anything Open Source. > > http://sourceforge.net/services/buy/index.php > > ___ > > The BASE general discussion mailing list > > basedb-users@lists.sourceforge.net > > unsubscribe: send a mail with subject "unsubscribe" to > > [EMAIL PROTECTED] > - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
[base] lowess normalisation
I've done some more tests on the lowess problem. Please refer from now on to our development server: http://base.vectorbase.org:8080/base2dev/ Experiment: "Male vs. female (Koutsos et al., 2007)" I ran the base1 lowess plugin and got a very different result compared to the base2 plugin. The base1 plugin results look correct to me. The base2 correction factor plots do not look at all right to me. Can anyone hazard a guess as to if this is a bug or are the default parameters not suitable for my data? Due to time pressures I think I'm going to have to switch all our analysis over to use the base1 plugin. many thanks, Bob. Bob MacCallum writes: > > Has anyone had problems with the Lowess analysis plugin? > > To me it looks like it is overcorrecting. Where a M/A plot > is largely below the zero line before normalisation, it ends > up largely above it afterwards. > > I'm using default values (including 0 for block group size). > Default values were always fine in BASE1. > > You can look for yourself with the guest login at > http://fungen.vectorbase.org/base2 > > Experiment "Male vs. female (Koutsos et al., 2007)" is a good > small example. > > I don't see a recent ticket on this (I have not upgraded in > a few months). > > cheers, > Bob. > > > -- > Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | > Division of Cell and Molecular Biology | Imperial College London | > Phone +442075941945 | Email [EMAIL PROTECTED] > > - > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://sourceforge.net/services/buy/index.php > ___ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED] - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
[base] lowess normalisation
Has anyone had problems with the Lowess analysis plugin? To me it looks like it is overcorrecting. Where a M/A plot is largely below the zero line before normalisation, it ends up largely above it afterwards. I'm using default values (including 0 for block group size). Default values were always fine in BASE1. You can look for yourself with the guest login at http://fungen.vectorbase.org/base2 Experiment "Male vs. female (Koutsos et al., 2007)" is a good small example. I don't see a recent ticket on this (I have not upgraded in a few months). cheers, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED] - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
