Suggestions on Agilent gene expression data
3
0
Entering edit mode
affy snp ▴ 640
@affy-snp-2480
Last seen 10.2 years ago
Dear all, For whom is familiar with Agilent gene expression data, I would like to ask help. We recently received some Agilent gene expression data from our collaborators. For individual sample, there are 7 corresponding columns: Unknown:Log(Ratio) Unknown:Ratio Unknown:Fold Change Unknown:Log(Error) Unknown:P-Value Unknown:Intensity 1 Unknown:Intensity 2 It seems that Ratio= Intensity1/Intensity2. I wonder whether I should use log2(Ratio) or Log(Ratio) or just Ratio for further analysis. Besides, why should Ratio be calculated as Intensity1/Intensity2 instead of Intensity2/Intensity1? Thank you very much for your help in advance! Sincerely, Allen [[alternative HTML version deleted]]
• 1.8k views
ADD COMMENT •
0
Entering edit mode
@sean-davis-490
Last seen 3 months ago
United States
On Wed, Jun 11, 2008 at 7:43 PM, ss <affysnp at="" gmail.com=""> wrote: > Dear all, > > For whom is familiar with Agilent gene expression data, I would like to > ask help. > > We recently received some Agilent gene expression data from our > collaborators. For individual sample, there are 7 corresponding columns: > > Unknown:Log(Ratio) Unknown:Ratio Unknown:Fold Change Unknown:Log(Error) > Unknown:P-Value Unknown:Intensity 1 Unknown:Intensity 2 > It seems that Ratio= Intensity1/Intensity2. I wonder whether I should use > log2(Ratio) or Log(Ratio) or just Ratio for further analysis. Besides, why > should Ratio be calculated as Intensity1/Intensity2 instead of > Intensity2/Intensity1? Hi, Allen. You'll probably need to do some quality control and some normalization. The choice of ratio is arbitrary; you can always invert it if it is more convenient to do so. As for log2 or log, they are equivalent to each other with the exception of a constant. You might look at the limma manual for some guidance on working with two-color arrays. Sean
ADD COMMENT •
0
Entering edit mode
Hi Sean, Thanks a lot! The data we downloaded has already been normalized and processed. So I guess I can go ahead without further quality control. My question then is that if I want to utilize some other tools or softwares for higher level analysis, should I use ratio, or log2(ratio) or Log(ratio)? Or it does not matter at all? Best, Allen On Wed, Jun 11, 2008 at 10:01 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > On Wed, Jun 11, 2008 at 7:43 PM, ss <affysnp@gmail.com> wrote: > > Dear all, > > > > For whom is familiar with Agilent gene expression data, I would like to > > ask help. > > > > We recently received some Agilent gene expression data from our > > collaborators. For individual sample, there are 7 corresponding columns: > > > > Unknown:Log(Ratio) Unknown:Ratio Unknown:Fold Change > Unknown:Log(Error) > > Unknown:P-Value Unknown:Intensity 1 Unknown:Intensity 2 > > It seems that Ratio= Intensity1/Intensity2. I wonder whether I should use > > log2(Ratio) or Log(Ratio) or just Ratio for further analysis. Besides, > why > > should Ratio be calculated as Intensity1/Intensity2 instead of > > Intensity2/Intensity1? > > Hi, Allen. You'll probably need to do some quality control and some > normalization. The choice of ratio is arbitrary; you can always > invert it if it is more convenient to do so. As for log2 or log, they > are equivalent to each other with the exception of a constant. You > might look at the limma manual for some guidance on working with > two-color arrays. > > Sean > [[alternative HTML version deleted]]
ADD REPLY •
0
Entering edit mode
Hi Allen, you'll want to use either the log2(ratio) or the log(ratio). As Sean said, they're equivalent up to a constant. Basically all the BioC packages (and most of the other tools) expect logged data, especially when it is pre-normalized. Many people tend to use log2, as they're easier to interpret directly (easier to multiply in your head by 2 than by e) and the scanner generally gives values that are 1-2^16. Francois ss wrote: > Hi Sean, > > Thanks a lot! The data we downloaded has already been normalized and > processed. > So I guess I can go ahead without further quality control. My question then > is that > if I want to utilize some other tools or softwares for higher level > analysis, should I use > ratio, or log2(ratio) or Log(ratio)? Or it does not matter at all? > > Best, > Allen > > > > On Wed, Jun 11, 2008 at 10:01 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > >> On Wed, Jun 11, 2008 at 7:43 PM, ss <affysnp at="" gmail.com=""> wrote: >>> Dear all, >>> >>> For whom is familiar with Agilent gene expression data, I would like to >>> ask help. >>> >>> We recently received some Agilent gene expression data from our >>> collaborators. For individual sample, there are 7 corresponding columns: >>> >>> Unknown:Log(Ratio) Unknown:Ratio Unknown:Fold Change >> Unknown:Log(Error) >>> Unknown:P-Value Unknown:Intensity 1 Unknown:Intensity 2 >>> It seems that Ratio= Intensity1/Intensity2. I wonder whether I should use >>> log2(Ratio) or Log(Ratio) or just Ratio for further analysis. Besides, >> why >>> should Ratio be calculated as Intensity1/Intensity2 instead of >>> Intensity2/Intensity1? >> Hi, Allen. You'll probably need to do some quality control and some >> normalization. The choice of ratio is arbitrary; you can always >> invert it if it is more convenient to do so. As for log2 or log, they >> are equivalent to each other with the exception of a constant. You >> might look at the limma manual for some guidance on working with >> two-color arrays. >> >> Sean >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLY •
0
Entering edit mode
On Wed, Jun 11, 2008 at 10:15 PM, ss <affysnp at="" gmail.com=""> wrote: > Hi Sean, > > Thanks a lot! The data we downloaded has already been normalized and > processed. > So I guess I can go ahead without further quality control. I would not make the assumption that all is well with the data without looking at some plots, etc., but I suppose that it depends on what you are doing with the data and how much you care about the results. > My question then > is that > if I want to utilize some other tools or softwares for higher level > analysis, should I use > ratio, or log2(ratio) or Log(ratio)? Or it does not matter at all? > On Wed, Jun 11, 2008 at 10:01 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > >> On Wed, Jun 11, 2008 at 7:43 PM, ss <affysnp at="" gmail.com=""> wrote: >> > Dear all, >> > >> > For whom is familiar with Agilent gene expression data, I would like to >> > ask help. >> > >> > We recently received some Agilent gene expression data from our >> > collaborators. For individual sample, there are 7 corresponding columns: >> > >> > Unknown:Log(Ratio) Unknown:Ratio Unknown:Fold Change >> Unknown:Log(Error) >> > Unknown:P-Value Unknown:Intensity 1 Unknown:Intensity 2 >> > It seems that Ratio= Intensity1/Intensity2. I wonder whether I should use >> > log2(Ratio) or Log(Ratio) or just Ratio for further analysis. Besides, >> why >> > should Ratio be calculated as Intensity1/Intensity2 instead of >> > Intensity2/Intensity1? >> >> Hi, Allen. You'll probably need to do some quality control and some >> normalization. The choice of ratio is arbitrary; you can always >> invert it if it is more convenient to do so. As for log2 or log, they >> are equivalent to each other with the exception of a constant. You >> might look at the limma manual for some guidance on working with >> two-color arrays. >> >> Sean >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLY •
0
Entering edit mode
@kasper-daniel-hansen-2979
Last seen 17 months ago
United States
This does not look at all like an Agilent data file from Feature Extractor. I suggest you contact your collaborators and get an idea about what you should use. Kasper On Jun 11, 2008, at 4:43 PM, ss wrote: > Dear all, > > For whom is familiar with Agilent gene expression data, I would like > to > ask help. > > We recently received some Agilent gene expression data from our > collaborators. For individual sample, there are 7 corresponding > columns: > > Unknown:Log(Ratio) Unknown:Ratio Unknown:Fold Change > Unknown:Log(Error) > Unknown:P-Value Unknown:Intensity 1 Unknown:Intensity 2 > It seems that Ratio= Intensity1/Intensity2. I wonder whether I > should use > log2(Ratio) or Log(Ratio) or just Ratio for further analysis. > Besides, why > should Ratio be calculated as Intensity1/Intensity2 instead of > Intensity2/Intensity1? > > Thank you very much for your help in advance! > > Sincerely, > Allen > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENT •
0
Entering edit mode
Thanks Kasper. We downloaded the processed data under the accession number 'E-TABM-1' from ArrayExpress at http://www.ebi.ac.uk/microarray-as/aer/#ae-browse/q=E-TABM-1[2] So if you click 'E-TABM-1' and it says that: Array:Agilent Whole Human Genome Oligo Microarray [G4112A] (» A-AGIL-11<http: www.ebi.ac.uk="" microarray-="" as="" aer="" result?queryfor="PhysicalArrayDesign&amp;aAccession=A%2DAGIL%2D11"> ) I guess it is of Agilent format for sure. What does it seem strange to you? Allen On Fri, Jun 13, 2008 at 11:05 PM, Kasper Daniel Hansen < khansen@stat.berkeley.edu> wrote: > This does not look at all like an Agilent data file from Feature Extractor. > I suggest you contact your collaborators and get an idea about what you > should use. > > Kasper > > > On Jun 11, 2008, at 4:43 PM, ss wrote: > > Dear all, >> >> For whom is familiar with Agilent gene expression data, I would like to >> ask help. >> >> We recently received some Agilent gene expression data from our >> collaborators. For individual sample, there are 7 corresponding columns: >> >> Unknown:Log(Ratio) Unknown:Ratio Unknown:Fold Change >> Unknown:Log(Error) >> Unknown:P-Value Unknown:Intensity 1 Unknown:Intensity 2 >> It seems that Ratio= Intensity1/Intensity2. I wonder whether I should use >> log2(Ratio) or Log(Ratio) or just Ratio for further analysis. Besides, why >> should Ratio be calculated as Intensity1/Intensity2 instead of >> Intensity2/Intensity1? >> >> Thank you very much for your help in advance! >> >> Sincerely, >> Allen >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]
ADD REPLY •
0
Entering edit mode
Just to follow up a bit, there are 7 corresponding columns for each sample. For instance, for the 1st array, they are: MBA: US14702370_16012391010920_S01_A01/Log(Ratio) MBA: US14702370_16012391010920_S01_A01/Ratio MBA: US14702370_16012391010920_S01_A01/Fold Change MBA: US14702370_16012391010920_S01_A01/Log(Error) MBA: US14702370_16012391010920_S01_A01/P-Value MBA: US14702370_16012391010920_S01_A01/Intensity 1 MBA: US14702370_16012391010920_S01_A01/Intensity 2 I figure I should use Ratio which is Intensity2/Intensity1 for further analysis. I really wish I could get started with raw data but I just dont know whether there is some packages for Agilent data. Allen On Fri, Jun 13, 2008 at 11:09 PM, ss <affysnp@gmail.com> wrote: > Thanks Kasper. We downloaded the processed data under the > accession number 'E-TABM-1' from ArrayExpress at > http://www.ebi.ac.uk/microarray-as/aer/#ae- browse/q=E-TABM-1[2]<http: www.ebi.ac.uk="" microarray-as="" aer="" #ae-="" browse="" q="E-TABM-1%5B2%5D"> > > So if you click 'E-TABM-1' and it says that: > > Array:Agilent Whole Human Genome Oligo Microarray [G4112A] (» A-AGIL-11<http: www.ebi.ac.uk="" microarray-="" as="" aer="" result?queryfor="PhysicalArrayDesign&amp;aAccession=A%2DAGIL%2D11"> > ) > I guess it is of Agilent format for sure. What does it seem strange to > you? > > Allen > > > > On Fri, Jun 13, 2008 at 11:05 PM, Kasper Daniel Hansen < > khansen@stat.berkeley.edu> wrote: > >> This does not look at all like an Agilent data file from Feature >> Extractor. I suggest you contact your collaborators and get an idea about >> what you should use. >> >> Kasper >> >> >> On Jun 11, 2008, at 4:43 PM, ss wrote: >> >> Dear all, >>> >>> For whom is familiar with Agilent gene expression data, I would like to >>> ask help. >>> >>> We recently received some Agilent gene expression data from our >>> collaborators. For individual sample, there are 7 corresponding columns: >>> >>> Unknown:Log(Ratio) Unknown:Ratio Unknown:Fold Change >>> Unknown:Log(Error) >>> Unknown:P-Value Unknown:Intensity 1 Unknown:Intensity 2 >>> It seems that Ratio= Intensity1/Intensity2. I wonder whether I should use >>> log2(Ratio) or Log(Ratio) or just Ratio for further analysis. Besides, >>> why >>> should Ratio be calculated as Intensity1/Intensity2 instead of >>> Intensity2/Intensity1? >>> >>> Thank you very much for your help in advance! >>> >>> Sincerely, >>> Allen >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> > [[alternative HTML version deleted]]
ADD REPLY •
0
Entering edit mode
As you said yourself, these are processed intensities, so how should we know what to do with them. It does not come out of Agilents software. But given these columns names I guess that - Ratio is equal to Intensity 1 / Intensity 2 (or vice verse) - Log(Ratio) is the logarithm of Ratio, check yourself to see what base they are using. My guess is either 2 or 10 but it could be e - I have no idea what Fold Change is, my guess would be that it is the same as Ratio - P value and log(error) are some kind of statistics associated with the hypothesis that intensity 1 is equal to intensity 2 - It is a two colour array. I would use Log(Ratio), checking to see what base it is in. Perhaps you can check out the raw files (which are probably Agilent files) and figure out what the columns are. They could correspond to something like gPorcessedSignal/rProcessedSignal Kasper On Jun 13, 2008, at 8:12 PM, ss wrote: > Just to follow up a bit, there are 7 corresponding columns for each > sample. > For instance, for the 1st array, they are: > > > MBA: US14702370_16012391010920_S01_A01/Log(Ratio) > MBA: US14702370_16012391010920_S01_A01/Ratio > MBA: US14702370_16012391010920_S01_A01/Fold Change > MBA: US14702370_16012391010920_S01_A01/Log(Error) > MBA: US14702370_16012391010920_S01_A01/P-Value > MBA: US14702370_16012391010920_S01_A01/Intensity 1 > MBA: US14702370_16012391010920_S01_A01/Intensity 2 > > I figure I should use Ratio which is Intensity2/Intensity1 for > further analysis. > I really wish I could get started with raw data but I just dont know > whether > there is some packages for Agilent data. > > Allen > > On Fri, Jun 13, 2008 at 11:09 PM, ss <affysnp@gmail.com> wrote: > Thanks Kasper. We downloaded the processed data under the > accession number 'E-TABM-1' from ArrayExpress at http://www.ebi.ac.uk/microarray-as/aer/#ae-browse/ > q=E-TABM-1[2] > > So if you click 'E-TABM-1' and it says that: > > Array: > Agilent Whole Human Genome Oligo Microarray [G4112A] (» A-AGIL-11) > I guess it is of Agilent format for sure. What does it seem strange to > you? > > Allen > > > > On Fri, Jun 13, 2008 at 11:05 PM, Kasper Daniel Hansen <khansen@stat.berkeley.edu> > wrote: > This does not look at all like an Agilent data file from Feature > Extractor. I suggest you contact your collaborators and get an idea > about what you should use. > > Kasper > > > On Jun 11, 2008, at 4:43 PM, ss wrote: > > Dear all, > > For whom is familiar with Agilent gene expression data, I would like > to > ask help. > > We recently received some Agilent gene expression data from our > collaborators. For individual sample, there are 7 corresponding > columns: > > Unknown:Log(Ratio) Unknown:Ratio Unknown:Fold Change > Unknown:Log(Error) > Unknown:P-Value Unknown:Intensity 1 Unknown:Intensity 2 > It seems that Ratio= Intensity1/Intensity2. I wonder whether I > should use > log2(Ratio) or Log(Ratio) or just Ratio for further analysis. > Besides, why > should Ratio be calculated as Intensity1/Intensity2 instead of > Intensity2/Intensity1? > > Thank you very much for your help in advance! > > Sincerely, > Allen > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > [[alternative HTML version deleted]]
ADD REPLY •
0
Entering edit mode
Kasper, Thanks! I checked and found that: Ratio = Intensity2/Intensity1 Log(Ratio) is based on 10 Since the data is already being processed, the quick and simple way to verify it is has been normalized could be to take the average of each array and see if they are very similar? I appreciate! Allen On Sat, Jun 14, 2008 at 1:08 AM, Kasper Daniel Hansen < khansen@stat.berkeley.edu> wrote: > As you said yourself, these are processed intensities, so how should we > know what to do with them. It does not come out of Agilents software. > But given these columns names I guess that > - Ratio is equal to Intensity 1 / Intensity 2 (or vice verse) > - Log(Ratio) is the logarithm of Ratio, check yourself to see what base > they are using. My guess is either 2 or 10 but it could be e > - I have no idea what Fold Change is, my guess would be that it is the > same as Ratio > - P value and log(error) are some kind of statistics associated with the > hypothesis that intensity 1 is equal to intensity 2 > - It is a two colour array. > > I would use Log(Ratio), checking to see what base it is in. > > Perhaps you can check out the raw files (which are probably Agilent files) > and figure out what the columns are. They could correspond to something like > gPorcessedSignal/rProcessedSignal > > Kasper > > On Jun 13, 2008, at 8:12 PM, ss wrote: > > Just to follow up a bit, there are 7 corresponding columns for each sample. > For instance, for the 1st array, they are: > > > MBA: US14702370_16012391010920_S01_A01/Log(Ratio) > MBA: US14702370_16012391010920_S01_A01/Ratio > MBA: US14702370_16012391010920_S01_A01/Fold Change > MBA: US14702370_16012391010920_S01_A01/Log(Error) > MBA: US14702370_16012391010920_S01_A01/P-Value > MBA: US14702370_16012391010920_S01_A01/Intensity 1 > MBA: US14702370_16012391010920_S01_A01/Intensity 2 > > I figure I should use Ratio which is Intensity2/Intensity1 for further > analysis. > I really wish I could get started with raw data but I just dont know > whether > there is some packages for Agilent data. > > Allen > > On Fri, Jun 13, 2008 at 11:09 PM, ss <affysnp@gmail.com> wrote: > >> Thanks Kasper. We downloaded the processed data under the >> accession number 'E-TABM-1' from ArrayExpress at >> http://www.ebi.ac.uk/microarray-as/aer/#ae- browse/q=E-TABM-1[2]<http: www.ebi.ac.uk="" microarray-as="" aer="" #ae-="" browse="" q="E-TABM-1%5B2%5D"> >> >> So if you click 'E-TABM-1' and it says that: >> >> Array:Agilent Whole Human Genome Oligo Microarray [G4112A] (» A-AGIL-11<http: www.ebi.ac.uk="" microarray-="" as="" aer="" result?queryfor="PhysicalArrayDesign&amp;aAccession=A%2DAGIL%2D11"> >> ) >> I guess it is of Agilent format for sure. What does it seem strange to >> you? >> >> Allen >> >> >> >> On Fri, Jun 13, 2008 at 11:05 PM, Kasper Daniel Hansen < >> khansen@stat.berkeley.edu> wrote: >> >>> This does not look at all like an Agilent data file from Feature >>> Extractor. I suggest you contact your collaborators and get an idea about >>> what you should use. >>> >>> Kasper >>> >>> >>> On Jun 11, 2008, at 4:43 PM, ss wrote: >>> >>> Dear all, >>>> >>>> For whom is familiar with Agilent gene expression data, I would like to >>>> ask help. >>>> >>>> We recently received some Agilent gene expression data from our >>>> collaborators. For individual sample, there are 7 corresponding columns: >>>> >>>> Unknown:Log(Ratio) Unknown:Ratio Unknown:Fold Change >>>> Unknown:Log(Error) >>>> Unknown:P-Value Unknown:Intensity 1 Unknown:Intensity 2 >>>> It seems that Ratio= Intensity1/Intensity2. I wonder whether I should >>>> use >>>> log2(Ratio) or Log(Ratio) or just Ratio for further analysis. Besides, >>>> why >>>> should Ratio be calculated as Intensity1/Intensity2 instead of >>>> Intensity2/Intensity1? >>>> >>>> Thank you very much for your help in advance! >>>> >>>> Sincerely, >>>> Allen >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor@stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >>> >> > > [[alternative HTML version deleted]]
ADD REPLY •
0
Entering edit mode
Mark Cowley ▴ 400
@mark-cowley-2858
Last seen 9.2 years ago
Australia
Hi Allen (we should keep this conversation on the list). yes, normalized intensity 1 and 2 would be a good place to start for making MA plots. If you haven't made MA plots before, i'd suggest looking through the limma user guide. I'd recommend making a pdf file with 3x3 rows and columns, then plotting all 83 of them (thus 10 pages of output). In addition, a boxplot of the ratios (in log2 space) will reveal whether these ratios have similar distributions. cheers, Mark On 16/06/2008, at 10:18 AM, ss wrote: > Hi Mark, > > Thanks much! So I should get started with normalized intensity 1 and > intensity2, right? > There are 83 arrays and what is the best way to assess MA plot? One > by one? > > Best, > Allen > > On Sun, Jun 15, 2008 at 7:41 PM, Mark Cowley <m.cowley0@gmail.com> > wrote: > Hi Allen, > > Since you also have intensity 1 and intensity 2 columns, you can > perform MA plots of your data; for me, this would be the most > revealing way of identifying how normalised the data is. > > Boxplots, or density plots of the ratios should give you a good idea > of whether the ratios are symmetrically distributed > > cheers, > Mark > > > On 14/06/2008, at 3:32 PM, ss wrote: > > Kasper, > > Thanks! > > I checked and found that: > > Ratio = Intensity2/Intensity1 > > Log(Ratio) is based on 10 > > Since the data is already being processed, the quick and simple way to > verify it is has been > normalized could be to take the average of each array and see if > they are > very similar? > > I appreciate! > > Allen > > On Sat, Jun 14, 2008 at 1:08 AM, Kasper Daniel Hansen < > khansen@stat.berkeley.edu> wrote: > > As you said yourself, these are processed intensities, so how should > we > know what to do with them. It does not come out of Agilents software. > But given these columns names I guess that > - Ratio is equal to Intensity 1 / Intensity 2 (or vice verse) > - Log(Ratio) is the logarithm of Ratio, check yourself to see what > base > they are using. My guess is either 2 or 10 but it could be e > - I have no idea what Fold Change is, my guess would be that it is the > same as Ratio > - P value and log(error) are some kind of statistics associated with > the > hypothesis that intensity 1 is equal to intensity 2 > - It is a two colour array. > > I would use Log(Ratio), checking to see what base it is in. > > Perhaps you can check out the raw files (which are probably Agilent > files) > and figure out what the columns are. They could correspond to > something like > gPorcessedSignal/rProcessedSignal > > Kasper > > On Jun 13, 2008, at 8:12 PM, ss wrote: > > Just to follow up a bit, there are 7 corresponding columns for each > sample. > For instance, for the 1st array, they are: > > > MBA: US14702370_16012391010920_S01_A01/Log(Ratio) > MBA: US14702370_16012391010920_S01_A01/Ratio > MBA: US14702370_16012391010920_S01_A01/Fold Change > MBA: US14702370_16012391010920_S01_A01/Log(Error) > MBA: US14702370_16012391010920_S01_A01/P-Value > MBA: US14702370_16012391010920_S01_A01/Intensity 1 > MBA: US14702370_16012391010920_S01_A01/Intensity 2 > > I figure I should use Ratio which is Intensity2/Intensity1 for further > analysis. > I really wish I could get started with raw data but I just dont know > whether > there is some packages for Agilent data. > > Allen > > On Fri, Jun 13, 2008 at 11:09 PM, ss <affysnp@gmail.com> wrote: > > Thanks Kasper. We downloaded the processed data under the > accession number 'E-TABM-1' from ArrayExpress at > http://www.ebi.ac.uk/microarray-as/aer/#ae- browse/q=E-TABM-1[2]<http: www.ebi.ac.uk="" microarray-as="" aer="" #ae-="" browse="" q="E-TABM-1%5B2%5D"> > > > > So if you click 'E-TABM-1' and it says that: > > Array:Agilent Whole Human Genome Oligo Microarray [G4112A] (» A- > AGIL-11<http: www.ebi.ac.uk="" microarray-="" as="" aer="" result?queryfor="PhysicalArrayDesign&amp;aAccession=A%2DAGIL%2D11"> > > > ) > I guess it is of Agilent format for sure. What does it seem strange to > you? > > Allen > > > > On Fri, Jun 13, 2008 at 11:05 PM, Kasper Daniel Hansen < > khansen@stat.berkeley.edu> wrote: > > This does not look at all like an Agilent data file from Feature > Extractor. I suggest you contact your collaborators and get an idea > about > what you should use. > > Kasper > > > On Jun 11, 2008, at 4:43 PM, ss wrote: > > Dear all, > > For whom is familiar with Agilent gene expression data, I would like > to > ask help. > > We recently received some Agilent gene expression data from our > collaborators. For individual sample, there are 7 corresponding > columns: > > Unknown:Log(Ratio) Unknown:Ratio Unknown:Fold Change > Unknown:Log(Error) > Unknown:P-Value Unknown:Intensity 1 Unknown:Intensity 2 > It seems that Ratio= Intensity1/Intensity2. I wonder whether I should > use > log2(Ratio) or Log(Ratio) or just Ratio for further analysis. Besides, > why > should Ratio be calculated as Intensity1/Intensity2 instead of > Intensity2/Intensity1? > > Thank you very much for your help in advance! > > Sincerely, > Allen > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]
ADD COMMENT •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 624 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6