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]]

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

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]]

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

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]]

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

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