DEXSeq plot error
0
0
Entering edit mode
@c5099c09
Last seen 5 months ago
France

Dear, I m using DEXSeq in order to analyse DEU. I got a result table with DEXSeq() function, I got many interesting differential exon usage with padj <0.05 but for one of them I got 2 exons with padj very low but in result table I got NA values for groups values and log2foldchange as:

groupID featureID exonBaseMean  dispersion     stat       pvalue         padj HC_ZT3 ORM1h
ENSMUSG00000005089:E001 ENSMUSG00000005089      E001     685.2941 0.001725370 33.03974 9.029436e-09 1.992781e-05     NA    NA
ENSMUSG00000005089:E034 ENSMUSG00000005089      E034   45712.1062 0.001449945 14.68005 1.273875e-04 4.215027e-02     NA    NA
                        log2fold_ORM1h_HC_ZT3 genomicData.seqnames genomicData.start genomicData.end genomicData.width genomicData.strand
ENSMUSG00000005089:E001                    NA                    2         102489004       102489567               564                  +
ENSMUSG00000005089:E034                    NA                    2         102612089       102621129              9041                  +
                        countData.NC_HC_AM1 countData.NC_HC_AM2 countData.NC_HC_AM3 countData.NC_HC_AM4 countData.NC_HC_AM5 countData.NC_HC_AM6
ENSMUSG00000005089:E001                 343                 301                 338                 356                 301                 398
ENSMUSG00000005089:E034               24285               24536               26479               28804               25330               33677
                        countData.NC_ORM1h1 countData.NC_ORM1h2 countData.NC_ORM1h3 countData.NC_ORM1h4 countData.NC_ORM1h5 countData.NC_ORM1h6
ENSMUSG00000005089:E001                1014                1221                1390                1099                 896                 822
ENSMUSG00000005089:E034               57453               78122               96298               68502               51991               49220
                         transcripts
ENSMUSG00000005089:E001 ENSMUST0....
ENSMUSG00000005089:E034 ENSMUST0....

with that result, I wanted to draw a plot with:

DTU_exon.usage_NC <- plotDEXSeq( dxr.fc_NC, "ENSMUSG00000005089", 
                             legend=TRUE, 
                             cex.axis=1.2, #1.2
                             cex=1.5, 
                             lwd=2,
                             color=c("#0000FF80", "#FF000080"),
                             expression=FALSE, 
                             splicing=TRUE,
                             displayTranscripts=TRUE)

and I got:

Fit for gene/exon ENSMUSG00000005089 threw the next warning(s): the matrix is either rank-deficient or indefinite

and

> plot(DTU_exon.usage_NC)
Error in plot.window(...) : 'xlim' nécessite des valeurs finies
In addition: Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
3: In min(x) : no non-missing arguments to min; returning Inf
4: In max(x) : no non-missing arguments to max; returning -Inf

Is there a solution to fix the issue? and something is strange because I could get a plot with the following code:

DTU_exon.usage_NC <- plotDEXSeq( dxr.fc_NC, "ENSMUSG00000005089", 
                             legend=TRUE, 
                             cex.axis=1.2, #1.2
                             cex=1.5, 
                             lwd=2,
                             color=c("#0000FF80", "#FF000080"),
                             expression=FALSE, 
                             splicing=FALSE,
                             displayTranscripts=TRUE,
                             norCounts = T)

enter image description here

Thanks in advance

-Jc

DEXSeq DEXSeqNAvalues DEXseq • 322 views

Login before adding your answer.

Traffic: 772 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6