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Question: uneven counts for edgeR
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gravatar for Lana Schaffer
7.1 years ago by
Lana Schaffer1.3k
Lana Schaffer1.3k wrote:
Hi, I have replicate sample counts for 2 groups but one sample is 4x number of mapped reads Than the other samples. 528,428 625,889 498,569 2,328,333 I divided all the mapped transcript reads by 4 and then did the normalization and analysis With edgeR. What do you recommend to do with the 4th sample counts? Lana Schaffer Biostatistics, Informatics DNA Array Core Facility 858-784-2263 [[alternative HTML version deleted]]
ADD COMMENTlink modified 7.1 years ago by Gordon Smyth35k • written 7.1 years ago by Lana Schaffer1.3k
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gravatar for Gordon Smyth
7.1 years ago by
Gordon Smyth35k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth35k wrote:
Dear Lana, edgeR has no difficulty with uneven library sizes, and will adjust for this automatically for this during the analysis. There is no need for you to do anything other than follow a standard analysis pipeline. You do not need to standardize the 4th sample by dividing the counts by dividing by 4, in fact you must not do this since it changes the mean-variance relationship for your data and invalidates the subsequent analysis. You need to input the true read counts into edgeR. Best wishes Gordon > Date: Fri, 21 Oct 2011 15:27:25 -0700 > From: Lana Schaffer <schaffer at="" scripps.edu=""> > To: "'bioconductor at r-project.org'" <bioconductor at="" r-project.org=""> > Subject: [BioC] uneven counts for edgeR > > Hi, > I have replicate sample counts for 2 groups but one sample is 4x number of mapped reads > Than the other samples. > 528,428 > > 625,889 > > 498,569 > > 2,328,333 > > I divided all the mapped transcript reads by 4 and then did the > normalization and analysis With edgeR. What do you recommend to do with > the 4th sample counts? > > Lana Schaffer > Biostatistics, Informatics > DNA Array Core Facility > 858-784-2263 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
ADD COMMENTlink written 7.1 years ago by Gordon Smyth35k
Gordon, Thank you for this information. Is the same true for DeSeq? Lana -----Original Message----- From: Gordon K Smyth [mailto:smyth@wehi.EDU.AU] Sent: Saturday, October 22, 2011 5:42 PM To: Lana Schaffer Cc: Bioconductor mailing list Subject: uneven counts for edgeR Dear Lana, edgeR has no difficulty with uneven library sizes, and will adjust for this automatically for this during the analysis. There is no need for you to do anything other than follow a standard analysis pipeline. You do not need to standardize the 4th sample by dividing the counts by dividing by 4, in fact you must not do this since it changes the mean-variance relationship for your data and invalidates the subsequent analysis. You need to input the true read counts into edgeR. Best wishes Gordon > Date: Fri, 21 Oct 2011 15:27:25 -0700 > From: Lana Schaffer <schaffer at="" scripps.edu=""> > To: "'bioconductor at r-project.org'" <bioconductor at="" r-project.org=""> > Subject: [BioC] uneven counts for edgeR > > Hi, > I have replicate sample counts for 2 groups but one sample is 4x number of mapped reads > Than the other samples. > 528,428 > > 625,889 > > 498,569 > > 2,328,333 > > I divided all the mapped transcript reads by 4 and then did the > normalization and analysis With edgeR. What do you recommend to do with > the 4th sample counts? > > Lana Schaffer > Biostatistics, Informatics > DNA Array Core Facility > 858-784-2263 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:6}}
ADD REPLYlink written 7.1 years ago by Lana Schaffer1.3k
Gordon Smyth wrote: > edgeR has no difficulty with uneven library sizes, and will adjust for > this automatically for this during the analysis. There is no need > for you to do anything other than follow a standard analysis pipeline. Lana Schaffer wrote: > Is the same true for DeSeq? Yes, it is. Simon
ADD REPLYlink written 7.1 years ago by Simon Anders3.5k
Gordon, An unnamed company is claiming that the RPKM counts and/or Some transformation of the RPKM counts is 90% normal, 5% NB, And 5% poisson distribution using the Akaiki Information Criteria. Can you explain why this is or is not plausable? Lana -----Original Message----- From: Gordon K Smyth [mailto:smyth@wehi.EDU.AU] Sent: Saturday, October 22, 2011 5:42 PM To: Lana Schaffer Cc: Bioconductor mailing list Subject: uneven counts for edgeR Dear Lana, edgeR has no difficulty with uneven library sizes, and will adjust for this automatically for this during the analysis. There is no need for you to do anything other than follow a standard analysis pipeline. You do not need to standardize the 4th sample by dividing the counts by dividing by 4, in fact you must not do this since it changes the mean-variance relationship for your data and invalidates the subsequent analysis. You need to input the true read counts into edgeR. Best wishes Gordon > Date: Fri, 21 Oct 2011 15:27:25 -0700 > From: Lana Schaffer <schaffer at="" scripps.edu=""> > To: "'bioconductor at r-project.org'" <bioconductor at="" r-project.org=""> > Subject: [BioC] uneven counts for edgeR > > Hi, > I have replicate sample counts for 2 groups but one sample is 4x number of mapped reads > Than the other samples. > 528,428 > > 625,889 > > 498,569 > > 2,328,333 > > I divided all the mapped transcript reads by 4 and then did the > normalization and analysis With edgeR. What do you recommend to do with > the 4th sample counts? > > Lana Schaffer > Biostatistics, Informatics > DNA Array Core Facility > 858-784-2263 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:6}}
ADD REPLYlink written 7.1 years ago by Lana Schaffer1.3k
Dear Lana, It sounds strange, but it would be unwise for me to comment without knowing what they mean. It is of course technically impossible for RPKM to be negative binomial or Poisson because RPKM values are not integers. Best wishes Gordon --------------------------------------------- Professor Gordon K Smyth, Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Vic 3052, Australia. smyth at wehi.edu.au http://www.wehi.edu.au http://www.statsci.org/smyth On Wed, 26 Oct 2011, Lana Schaffer wrote: > Gordon, > An unnamed company is claiming that the RPKM counts and/or > Some transformation of the RPKM counts is 90% normal, 5% NB, > And 5% poisson distribution using the Akaiki Information Criteria. > Can you explain why this is or is not plausable? > > Lana > > -----Original Message----- > From: Gordon K Smyth [mailto:smyth at wehi.EDU.AU] > Sent: Saturday, October 22, 2011 5:42 PM > To: Lana Schaffer > Cc: Bioconductor mailing list > Subject: uneven counts for edgeR > > Dear Lana, > > edgeR has no difficulty with uneven library sizes, and will adjust for > this automatically for this during the analysis. There is no need for you > to do anything other than follow a standard analysis pipeline. > > You do not need to standardize the 4th sample by dividing the counts by > dividing by 4, in fact you must not do this since it changes the > mean-variance relationship for your data and invalidates the subsequent > analysis. You need to input the true read counts into edgeR. > > Best wishes > Gordon > > >> Date: Fri, 21 Oct 2011 15:27:25 -0700 >> From: Lana Schaffer <schaffer at="" scripps.edu=""> >> To: "'bioconductor at r-project.org'" <bioconductor at="" r-project.org=""> >> Subject: [BioC] uneven counts for edgeR >> >> Hi, >> I have replicate sample counts for 2 groups but one sample is 4x number of mapped reads >> Than the other samples. >> 528,428 >> >> 625,889 >> >> 498,569 >> >> 2,328,333 >> >> I divided all the mapped transcript reads by 4 and then did the >> normalization and analysis With edgeR. What do you recommend to do with >> the 4th sample counts? >> >> Lana Schaffer >> Biostatistics, Informatics >> DNA Array Core Facility >> 858-784-2263 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
ADD REPLYlink written 7.1 years ago by Gordon Smyth35k
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