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  • dpryan
    replied
    What happens if you do this instead: des <- ~sampleCondition

    Leave a comment:


  • essepf
    replied
    DESeq2 --- htseq-count

    Hi Michael

    Thank you for your suggestion......

    Originally posted by Michael Love View Post
    hi essepf,

    Did you check the length of the count files, as Devon recommended above?

    Yes...all files have 38932....

    What does sampleCondition look like?

    > sampleCondition
    [1] pr pr pr wt wt wt
    Levels: pr wt


    What's your sessionInfo()

    > sessionInfo()
    R version 3.1.0 (2014-04-10)
    Platform: x86_64-apple-darwin13.1.0 (64-bit)

    locale:
    [1] C

    attached base packages:
    [1] parallel stats graphics grDevices utils datasets methods base

    other attached packages:
    [1] BiocInstaller_1.14.2 gplots_2.14.1 ggplot2_1.0.0 DESeq_1.16.0 lattice_0.20-29 locfit_1.5-9.1 Biobase_2.24.0
    [8] DESeq2_1.4.5 RcppArmadillo_0.4.320.0 Rcpp_0.11.2 GenomicRanges_1.16.4 GenomeInfoDb_1.0.2 IRanges_1.22.10 BiocGenerics_0.10.0

    loaded via a namespace (and not attached):
    [1] AnnotationDbi_1.26.0 DBI_0.2-7 KernSmooth_2.23-12 MASS_7.3-33 RColorBrewer_1.0-5 RSQLite_0.11.4 XML_3.98-1.1 XVector_0.4.0
    [9] annotate_1.42.1 bitops_1.0-6 caTools_1.17 colorspace_1.2-4 digest_0.6.4 gdata_2.13.3 genefilter_1.46.1 geneplotter_1.42.0
    [17] grid_3.1.0 gtable_0.1.2 gtools_3.4.1 munsell_0.4.2 plyr_1.8.1 proto_0.3-10 reshape2_1.4 scales_0.2.4
    [25] splines_3.1.0 stats4_3.1.0 stringr_0.6.2 survival_2.37-7 tools_3.1.0 xtable_1.7-3

    Leave a comment:


  • Michael Love
    replied
    hi essepf,

    Did you check the length of the count files, as Devon recommended above?

    What does sampleCondition look like?

    What's your sessionInfo()

    Leave a comment:


  • essepf
    replied
    Hello I have more ou less the same problem:

    > ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory, design = des)
    Error in Ops.factor(a$V1, l[[1]]$V1) :
    level sets of factors are different

    the error is constantly on the factors but I'm not understand why.

    I have my ---- sampleCondition=factor and sampleTable=data.frame(sampleName=sampleFiles, fileName=sampleFiles,condition=sampleCondition)

    des <- formula(~ condition)

    I do not know if you can help with this error.

    Thank you very much

    Leave a comment:


  • pm2012
    replied
    Thanks a lot for help. It was indeed a problem with my count files. I didn't realize I had to redirect the output of HTseq into a different file. I was using file generated with -o option as an input.
    I reran the script & was able to generate the correct file (also filtered the last few lines starting with __). The rest of code seems to be working well now.
    I also got rid of last colum in sampleTable. It was just one of the many things I was trying to solve my issue.

    Leave a comment:


  • dpryan
    replied
    After a bit of poking around the source code, it looks like this might happen if there's something wrong with the count files, namely if they're different lengths. From the command line, you might run:

    Code:
    cut -f 1 231-un1-DESeq | sort | uniq -c
    If you compare the results of that file to the others the output of uniq -c, which just counts how many unique gene/feature names you have in a file, should be the same...but may not be for you.

    BTW, you can get rid of the last column of sampleTable ("stringAsFactors").

    Leave a comment:


  • pm2012
    replied
    Thanks for your reply.
    Here are the contents of sampleTable including the condition. I have 2 conditions with 2 replicates each.

    sampleNames sampleFiles condition stringAsFactors
    1 231un1 231-un1-DESeq un1 TRUE
    2 231un2 231-un2-DESeq un1 TRUE
    3 231trt1 231-trt1-DESeq trt2 TRUE
    4 231trt2 231-trt2-DESeq trt2 TRUE

    Here's the version info:

    > sessionInfo()
    R version 3.0.2 (2013-09-25)
    Platform: x86_64-pc-linux-gnu (64-bit)

    locale:
    [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
    [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
    [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
    [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
    [9] LC_ADDRESS=C LC_TELEPHONE=C
    [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

    attached base packages:
    [1] parallel stats graphics grDevices utils datasets methods
    [8] base

    other attached packages:
    [1] DESeq2_1.2.10 RcppArmadillo_0.4.200.0 Rcpp_0.11.1
    [4] GenomicRanges_1.14.4 XVector_0.2.0 IRanges_1.20.7
    [7] DESeq_1.14.0 lattice_0.20-24 locfit_1.5-9.1
    [10] Biobase_2.22.0 BiocGenerics_0.8.0

    loaded via a namespace (and not attached):
    [1] annotate_1.40.1 AnnotationDbi_1.24.0 DBI_0.2-7
    [4] genefilter_1.44.0 geneplotter_1.40.0 grid_3.0.2
    [7] RColorBrewer_1.0-5 RSQLite_0.11.4 splines_3.0.2
    [10] stats4_3.0.2 survival_2.37-7 XML_3.98-1.1
    [13] xtable_1.7-3

    Leave a comment:


  • dpryan
    replied
    That's a new one. What are the contents of "sampleTable" and "condition"? Also, which version (just type "sessionInfo()" and post the results)?
    Last edited by dpryan; 04-15-2014, 08:04 AM. Reason: Someday I'll reread things before posting...

    Leave a comment:


  • pm2012
    started a topic Error Running DESeq2

    Error Running DESeq2

    Hi

    I am trying to run DESeq2 using the reference manual provided in the bioconductor website. However I am running in the following error after this step: ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory, design= ~ condition) I created my count files using HTseq.

    Error msg.

    Error in Ops.factor(a$V1, l[[1]]$V1) : level sets of factors are different In addition: Warning message: In is.na(e1) | is.na(e2) : longer object length is not a multiple of shorter object length

    Any help is appreciated as I am both R/bioconductor and DESeq2 newbie.

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