Question: Important: Help with eBayes in AgiMicrRna and on how to find differentially expressed genes
0
gravatar for Karthik K N
7.8 years ago by
Karthik K N200
Karthik K N200 wrote:
Dear Lucas, I am using AgiMicroRna package and came across the same error that you also had i.e., Error in ebayes: No residual degrees of freedom in linear model fits. I read your posts<https: stat.ethz.ch="" pipermail="" bioconductor="" 2009-may="" 027834.html="">and the replies to that. My dataset consists of just 2 different arrays, one control and one treated. I am trying to find out diferentially expressed genes between them. >From the reply to your post I understood the reason why I am seeing this error with eBayes. I just wanted to ask help from you on how will I be able to find out differentially expressed genes between these datasets? I saw you mentioning BGX, but will that work with Agilent miRNA microarray platform? My idea is that it will not. If there is there anything that you can do to help me solve this, I will be really thankful to you. Thank you Karthik. -- Karthik K.N [[alternative HTML version deleted]]
bgx agimicrorna • 636 views
ADD COMMENTlink modified 7.8 years ago by Lucas Santana dos Santos60 • written 7.8 years ago by Karthik K N200
Answer: Important: Help with eBayes in AgiMicrRna and on how to find differentially expr
0
gravatar for Sean Davis
7.8 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Mon, Feb 6, 2012 at 8:29 AM, Karthik K N <karthikuttan at="" gmail.com=""> wrote: > Dear Lucas, > > I am using AgiMicroRna package and came across the same error that you also > had i.e., Error in ebayes: No residual degrees of freedom in linear model > fits. > > I read your posts<https: stat.ethz.ch="" pipermail="" bioconductor="" 2009-m="" ay="" 027834.html="">and > the replies to that. > > My dataset consists of just 2 different arrays, one control and one > treated. I am trying to find out diferentially expressed genes between > them. > > >From the reply to your post I understood the reason why I am seeing this > error with eBayes. I just wanted to ask help from you on how will I be able > to find out differentially expressed genes between these datasets? > > I saw you mentioning BGX, but will that work with Agilent miRNA microarray > platform? My idea is that it will not. > > If there is there anything that you can do to help me solve this, I will be > really thankful to you. Hi, Karthik. The "No residual degrees of freedom" in your case is statistical language meaning that you do not have enough samples to perform the number of tests you want to perform. In your case, this is a problem because it is not possible to do a statistical hypothesis test with only two samples. This is not a software problem but a statistical issue. To "fix" the problem, you will need to perform some biologic replicates. To deal with your data as-is, you can simply compute a ratio between treatment and control. Sean
ADD COMMENTlink written 7.8 years ago by Sean Davis21k
Dear Sean, Thank you for your reply. At this time, I am left with no choice but to deal with the data as-is. I realize that it is hard to work without replicates, but is there any way to make maximum meaningful info from this limited data set that I have? Some other tools/algorithms/packages/tests? Also, what does the contents of ProcessedData.txt file exported from AgiMicroRna mean? As far as I know, they are the Total Gene Signals of all those miRNAs that pass the filtering step. Isn't it? So, what downstream tests can I do using it as an input file? As mentioned in my previous post, I am interested in finding out the differentially expressed genes between my control and treated samples. Thanks a lot again. Karthik On Mon, Feb 6, 2012 at 7:21 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > On Mon, Feb 6, 2012 at 8:29 AM, Karthik K N <karthikuttan@gmail.com> > wrote: > > Dear Lucas, > > > > I am using AgiMicroRna package and came across the same error that you > also > > had i.e., Error in ebayes: No residual degrees of freedom in linear model > > fits. > > > > I read your posts< > https://stat.ethz.ch/pipermail/bioconductor/2009-May/027834.html>and > > the replies to that. > > > > My dataset consists of just 2 different arrays, one control and one > > treated. I am trying to find out diferentially expressed genes between > > them. > > > > >From the reply to your post I understood the reason why I am seeing this > > error with eBayes. I just wanted to ask help from you on how will I be > able > > to find out differentially expressed genes between these datasets? > > > > I saw you mentioning BGX, but will that work with Agilent miRNA > microarray > > platform? My idea is that it will not. > > > > If there is there anything that you can do to help me solve this, I will > be > > really thankful to you. > > Hi, Karthik. > > The "No residual degrees of freedom" in your case is statistical > language meaning that you do not have enough samples to perform the > number of tests you want to perform. In your case, this is a problem > because it is not possible to do a statistical hypothesis test with > only two samples. This is not a software problem but a statistical > issue. To "fix" the problem, you will need to perform some biologic > replicates. > > To deal with your data as-is, you can simply compute a ratio between > treatment and control. > > Sean > -- Karthik K.N [[alternative HTML version deleted]]
ADD REPLYlink written 7.8 years ago by Karthik K N200
On Mon, Feb 6, 2012 at 9:15 AM, Karthik K N <karthikuttan at="" gmail.com=""> wrote: > Dear Sean, > > Thank you for your reply. At this time, I am left with no choice but to > deal with the data as-is. I realize that it is hard to work without > replicates, but is there any way to make maximum meaningful info from this > limited data set that I have? Some other tools/algorithms/packages/tests? > > Also, what does the contents of ProcessedData.txt file exported from > AgiMicroRna mean? As far as I know, they are the Total Gene Signals of all > those miRNAs that pass the filtering step. Isn't it? So, what downstream > tests can I do using it as an input file? As mentioned in my previous post, > I am interested in finding out the differentially expressed genes between > my control and treated samples. Hi, Karthik. I'd suggest making a ratio of the treatment versus control. Those probes that show a large fold change are the candidates showing differential expression. The cutoff for fold-change will be experiment-specific, so you'll have to look at your data. Just out of curiosity, what is the reason for the inability to generate replicates? If cost is an issue, It is important to realize that NOT generating replicates can be more costly than actually generating them, depending on what your followup for candidate differentially expressed genes will be. Sean > On Mon, Feb 6, 2012 at 7:21 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > >> On Mon, Feb 6, 2012 at 8:29 AM, Karthik K N <karthikuttan at="" gmail.com=""> >> wrote: >> > Dear Lucas, >> > >> > I am using AgiMicroRna package and came across the same error that you >> also >> > had i.e., Error in ebayes: No residual degrees of freedom in linear model >> > fits. >> > >> > I read your posts< >> https://stat.ethz.ch/pipermail/bioconductor/2009-May/027834.html>and >> > the replies to that. >> > >> > My dataset consists of just 2 different arrays, one control and one >> > treated. I am trying to find out diferentially expressed genes between >> > them. >> > >> > >From the reply to your post I understood the reason why I am seeing this >> > error with eBayes. I just wanted to ask help from you on how will I be >> able >> > to find out differentially expressed genes between these datasets? >> > >> > I saw you mentioning BGX, but will that work with Agilent miRNA >> microarray >> > platform? My idea is that it will not. >> > >> > If there is there anything that you can do to help me solve this, I will >> be >> > really thankful to you. >> >> Hi, Karthik. >> >> The "No residual degrees of freedom" in your case is statistical >> language meaning that you do not have enough samples to perform the >> number of tests you want to perform. ?In your case, this is a problem >> because it is not possible to do a statistical hypothesis test with >> only two samples. ?This is not a software problem but a statistical >> issue. ?To "fix" the problem, you will need to perform some biologic >> replicates. >> >> To deal with your data as-is, you can simply compute a ratio between >> treatment and control. >> >> Sean >> > > > > -- > Karthik K.N > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 7.8 years ago by Sean Davis21k
Answer: Important: Help with eBayes in AgiMicrRna and on how to find differentially expr
0
gravatar for Lucas Santana dos Santos
7.8 years ago by
Hi Karthik, Since you have two groups, if could use a simple t-test and correct the p-values for multiple testing using Benjamin-hochberg. Besides the t-test, I would suggest to you the sam.r package to find the differentially expressed genes. I have never use BGX with agilent, so I am not sure that this would work. Let me know if you need further help. Best, Lucas On Feb 6, 2012, at 8:29 AM, Karthik K N wrote: > Dear Lucas, > > I am using AgiMicroRna package and came across the same error that you also had i.e., Error in ebayes: No residual degrees of freedom in linear model fits. > > I read your posts and the replies to that. > > My dataset consists of just 2 different arrays, one control and one treated. I am trying to find out diferentially expressed genes between them. > > From the reply to your post I understood the reason why I am seeing this error with eBayes. I just wanted to ask help from you on how will I be able to find out differentially expressed genes between these datasets? > > I saw you mentioning BGX, but will that work with Agilent miRNA microarray platform? My idea is that it will not. > > If there is there anything that you can do to help me solve this, I will be really thankful to you. > > > Thank you > > Karthik. > -- > Karthik K.N > > [[alternative HTML version deleted]]
ADD COMMENTlink written 7.8 years ago by Lucas Santana dos Santos60
On Mon, Feb 6, 2012 at 9:26 AM, Lucas Santana dos Santos <lusasantos at="" gmail.com=""> wrote: > Hi Karthik, > > Since you have two groups, if could use a simple t-test and correct the p-values for multiple testing using Benjamin-hochberg. Besides the t-test, I would suggest to you the sam.r package to find the differentially expressed genes. > I have never use BGX with agilent, so I am not sure that this would work. Just so Karthik is not mislead, t-tests and other such hypothesis tests are not going to be useful without replicates. Sean > On Feb 6, 2012, at 8:29 AM, Karthik K N wrote: > >> Dear Lucas, >> >> I am using AgiMicroRna package and came across the same error that you also had i.e., Error in ebayes: No residual degrees of freedom in linear model fits. >> >> I read your posts and the replies to that. >> >> My dataset consists of just 2 different arrays, one control and one treated. I am trying to find out diferentially expressed genes between them. >> >> From the reply to your post I understood the reason why I am seeing this error with eBayes. I just wanted to ask help from you on how will I be able to find out differentially expressed genes between these datasets? >> >> I saw you mentioning BGX, but will that work with Agilent miRNA microarray platform? My idea is that it will not. >> >> If there is there anything that you can do to help me solve this, I will be really thankful to you. >> >> >> Thank you >> >> Karthik. >> -- >> Karthik K.N >> >> > > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 7.8 years ago by Sean Davis21k
Karthik, How does your data looks like? How many arrays do you have? I jumped in the middle of the thread, and did not get a description of you data. Lucas On Feb 6, 2012, at 9:33 AM, Sean Davis wrote: > On Mon, Feb 6, 2012 at 9:26 AM, Lucas Santana dos Santos > <lusasantos at="" gmail.com=""> wrote: >> Hi Karthik, >> >> Since you have two groups, if could use a simple t-test and correct the p-values for multiple testing using Benjamin-hochberg. Besides the t-test, I would suggest to you the sam.r package to find the differentially expressed genes. >> I have never use BGX with agilent, so I am not sure that this would work. > > Just so Karthik is not mislead, t-tests and other such hypothesis > tests are not going to be useful without replicates. > > Sean > > >> On Feb 6, 2012, at 8:29 AM, Karthik K N wrote: >> >>> Dear Lucas, >>> >>> I am using AgiMicroRna package and came across the same error that you also had i.e., Error in ebayes: No residual degrees of freedom in linear model fits. >>> >>> I read your posts and the replies to that. >>> >>> My dataset consists of just 2 different arrays, one control and one treated. I am trying to find out diferentially expressed genes between them. >>> >>> From the reply to your post I understood the reason why I am seeing this error with eBayes. I just wanted to ask help from you on how will I be able to find out differentially expressed genes between these datasets? >>> >>> I saw you mentioning BGX, but will that work with Agilent miRNA microarray platform? My idea is that it will not. >>> >>> If there is there anything that you can do to help me solve this, I will be really thankful to you. >>> >>> >>> Thank you >>> >>> Karthik. >>> -- >>> Karthik K.N >>> >>> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 7.8 years ago by Lucas Santana dos Santos60
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