Thread: [Jtreeview-users] Fwd: Clustering probem
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From: Alok S. <alo...@gm...> - 2010-01-31 13:11:39
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Hi Wendy, it looks like your data is not ratio data, but either count or intensity data. I got good results by logscaling with a center of 6 (this means a starting value x is mapped to y = log2(x / 6), i.e. a value of 6 is mapped to zero, and other values are turned into fold changes relative to 6. To do this, just open Settings->Pixel Settings, got the "LogScale" section below the contrast section, check "Log (base 2)" , and enter 6 as the center. If you clustered the samples, you should have an atr file which will provide an array tree. I strongly recommend you cluster the genes as well, as that will make it much easier to interpret the output. On Sun, Jan 31, 2010 at 7:41 AM, Wendy Qiao <wen...@ut...> wrote: > Hi Alok, > > > > Thank you for your reply. I think my values are too large. There are some > dots appearing after I increase the contrast value to the max (5), but I > still can’t see the map. Is there a way to navigate this? > > > > My cdt file is attach. I do not have a gtr file as I only clustered the > samples. Would that be one of the reason as well? > > > > Thank you . > > Wendy > > > > *From:* Alok Saldanha [mailto:alo...@gm...] > *Sent:* January-31-10 7:22 AM > *To:* Wendy Qiao > *Cc:* jtr...@li... > *Subject:* Re: [Jtreeview-users] Clustering probem > > > > Dear Wendy, > > This can sometimes happen if the values in your data file are outside of > the expected range. You can test this by selecting a few rows on the left > side of the screen and letting your mouse linger over the rows on the right > hand of the screen (i.e. the zoomed in rows). If the values displayed are > larger than 3, the you may need to adjust the contrast settings. To do this, > goto Settings->Pixel Settings, and either use the slider or edit the number > in the Contrast box. > > If this doesn't help, you can also send me a zip file containing the cdt > and gtr and I'll have a look. > > -Alok > > On Sat, Jan 30, 2010 at 7:29 AM, Wendy Qiao <wen...@ut...> > wrote: > > Dear there, > > > > When I try to cluster, the map is completely red. I think there is some > problem with the clustering algorithms that I used. I tried the most of the > Adjust Data-Cluster combinations in Cluster3.0, but no one works. What may > the possible reason? > > > > Thank you, > > Wendy > > > > > > > > ------------------------------------------------------------------------------ > The Planet: dedicated and managed hosting, cloud storage, colocation > Stay online with enterprise data centers and the best network in the > business > Choose flexible plans and management services without long-term contracts > Personal 24x7 support from experience hosting pros just a phone call away. > http://p.sf.net/sfu/theplanet-com > _______________________________________________ > Jtreeview-users mailing list > Jtr...@li... > https://lists.sourceforge.net/lists/listinfo/jtreeview-users > > > |
From: Alok S. <alo...@gm...> - 2010-01-31 14:10:29
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Dear Wendy, This can sometimes happen if the values in your data file are outside of the expected range. You can test this by selecting a few rows on the left side of the screen and letting your mouse linger over the rows on the right hand of the screen (i.e. the zoomed in rows). If the values displayed are larger than 3, the you may need to adjust the contrast settings. To do this, goto Settings->Pixel Settings, and either use the slider or edit the number in the Contrast box. If this doesn't help, you can also send me a zip file containing the cdt and gtr and I'll have a look. -Alok On Sat, Jan 30, 2010 at 7:29 AM, Wendy Qiao <wen...@ut...> wrote: > Dear there, > > > > When I try to cluster, the map is completely red. I think there is some > problem with the clustering algorithms that I used. I tried the most of the > Adjust Data-Cluster combinations in Cluster3.0, but no one works. What may > the possible reason? > > > > Thank you, > > Wendy > > > > > > > ------------------------------------------------------------------------------ > The Planet: dedicated and managed hosting, cloud storage, colocation > Stay online with enterprise data centers and the best network in the > business > Choose flexible plans and management services without long-term contracts > Personal 24x7 support from experience hosting pros just a phone call away. > http://p.sf.net/sfu/theplanet-com > _______________________________________________ > Jtreeview-users mailing list > Jtr...@li... > https://lists.sourceforge.net/lists/listinfo/jtreeview-users > > |