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Old 10-14-2012, 06:05 PM   #1
aprilw
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Location: Princeton, NJ

Join Date: May 2012
Posts: 8
Default Help Using DESeq without replicates

Hello,

I'm working with a data set that we have yet to replicate. I'm trying to take a cursory look at the differential expression, but I keep getting an error I don't understand. I don't know if it matters but I'm generating my count tables with HTSeq. Here is the error:

> table = read.delim(file="~/neuron_rna_seq/hypodermis_table.txt", header=FALSE, stringsAsFactors=TRUE)
> cds = newCountDataSetFromHTSeqCount(table, directory="~/neuron_rna_seq")
> cds = estimateSizeFactors( cds )
> sizeFactors( cds )
hypodermis hypodermis_unfiltered
0.3333333 3.0000000
> cds = estimateDispersions(cds, method="blind", sharingMode="fit-only")
Error in parametricDispersionFit(means, disps) :
Parametric dispersion fit failed. Try a local fit and/or a pooled estimation. (See '?estimateDispersions')
In addition: Warning message:
glm.fit: algorithm did not converge
#Because of this I use the local fit
> cds = estimateDispersions(cds, method="blind", sharingMode="fit-only", fitType="local")
> results = nbinomTest(cds, "hypodermis", "hypodermis_unfiltered")
#Error in question
Error in if (dispTable(cds)[condA] == "blind" || dispTable(cds)[condB] == :
missing value where TRUE/FALSE needed


I apologize if this is a basic question, I'm not an experienced user.

Thanks!
April
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Old 10-14-2012, 09:07 PM   #2
aprilw
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Location: Princeton, NJ

Join Date: May 2012
Posts: 8
Default Answer to my own question

Hi All,

Figures the first time I post a question I end up answering it myself.

My conditions were not named what I thought they were. I solved this by using dispTable(cds)[CondA]. With the incorrect condition name this evaluated to NA, thus causing the error.

Sorry for the stupid question, maybe this will help a similarly misguided person!
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Old 02-14-2013, 06:43 PM   #3
Pseudoknot
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Location: Australia

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Posts: 4
Default

It was useful, thanks!
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Old 06-04-2013, 04:02 PM   #4
indugun
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Location: India

Join Date: Apr 2013
Posts: 4
Default raju

Quote:
Originally Posted by aprilw View Post
Hello,

I'm working with a data set that we have yet to replicate. I'm trying to take a cursory look at the differential expression, but I keep getting an error I don't understand. I don't know if it matters but I'm generating my count tables with HTSeq. Here is the error:

> table = read.delim(file="~/neuron_rna_seq/hypodermis_table.txt", header=FALSE, stringsAsFactors=TRUE)
> cds = newCountDataSetFromHTSeqCount(table, directory="~/neuron_rna_seq")
> cds = estimateSizeFactors( cds )
> sizeFactors( cds )
hypodermis hypodermis_unfiltered
0.3333333 3.0000000
> cds = estimateDispersions(cds, method="blind", sharingMode="fit-only")
Error in parametricDispersionFit(means, disps) :
Parametric dispersion fit failed. Try a local fit and/or a pooled estimation. (See '?estimateDispersions')
In addition: Warning message:
glm.fit: algorithm did not converge
#Because of this I use the local fit
> cds = estimateDispersions(cds, method="blind", sharingMode="fit-only", fitType="local")
> results = nbinomTest(cds, "hypodermis", "hypodermis_unfiltered")
#Error in question
Error in if (dispTable(cds)[condA] == "blind" || dispTable(cds)[condB] == :
missing value where TRUE/FALSE needed


I apologize if this is a basic question, I'm not an experienced user.

Thanks!
April
Useful
Thank you
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Old 11-20-2013, 09:56 AM   #5
jeky82
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Location: Milan

Join Date: Jul 2013
Posts: 1
Default

I have the same error … but I did not understand how solve it, can you help me?
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Old 11-22-2013, 02:54 AM   #6
IsBeth
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Location: Spain

Join Date: Nov 2013
Posts: 28
Default

My pipeline in DEseq using data without replicates and 2 conditions is not working either. I thought that something was wrong with the dispersion. But no dispersion method works, so...maybe there's a problem with the preprocessing? Anybody got the same problem with DESeq?
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Old 12-19-2013, 07:07 AM   #7
choseqid
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Location: Europe

Join Date: Apr 2013
Posts: 5
Default

Hi April,

What exactly did you do with dispTable(cds)[CondA]?

Thanks.

Quote:
Originally Posted by aprilw View Post
Hi All,

Figures the first time I post a question I end up answering it myself.

My conditions were not named what I thought they were. I solved this by using dispTable(cds)[CondA]. With the incorrect condition name this evaluated to NA, thus causing the error.

Sorry for the stupid question, maybe this will help a similarly misguided person!
choseqid is offline   Reply With Quote
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