User: Miss Agnieszka Aleksandra Golicz

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40
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New User
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Australia
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5 days, 7 hours ago
Joined:
4 years, 7 months ago
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a***************@uq.net.au

Posts by Miss Agnieszka Aleksandra Golicz

<prev • 27 results • page 1 of 3 • next >
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Answer: A: Combat prior plots good enough?
... The non-parametric version just finished and the overlap is ~96%, so the answer most likely is the plots are good enough.  ...
written 14 months ago by Miss Agnieszka Aleksandra Golicz40
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Combat prior plots good enough?
... Hi, I read that the plots have to be really bad to cause a difference between parametric and non-parametric results, but I could not find any plots for comparison. Do you think with my plots I can still get away with using parametric ComBat? The url for plots: https://ibb.co/mMwMQb Any help would ...
combat combat sva written 14 months ago by Miss Agnieszka Aleksandra Golicz40
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OmicCircos barplot height and scale
... Hi, I'm trying to use OmicCircos to plot log(FPKM) as a barplot.  It seems to be working fine, other than the barplot seems to have a default height even if the the value of expression is 0. This can be seen when I add scale. 0 on the scale corresponds to an already sizable bar. This gives a false ...
omiccircos written 23 months ago by Miss Agnieszka Aleksandra Golicz40
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Comment: C: readVcf shape of 'skeleton' is not compatible with 'NROW(flesh)'
... Hi Valerie, After consulting this thread: https://support.bioconductor.org/p/67946/#68122 I have added FORMAT fields into the header. ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=DP,Number=1,Type=String,Description="Read Depth"> But readVcf() did not work ...
written 3.5 years ago by Miss Agnieszka Aleksandra Golicz40
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Comment: C: readVcf shape of 'skeleton' is not compatible with 'NROW(flesh)'
... I have share the file with you via cloudstore. You should have a link in your email box. Best wishes, Agnieszka ...
written 3.5 years ago by Miss Agnieszka Aleksandra Golicz40
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Comment: C: readVcf shape of 'skeleton' is not compatible with 'NROW(flesh)'
... Hi, I have used scanVcf() and it seems to have worked: > scn <- scanVcf(tab, param=param) > names(scn[[1]]) [1] "rowRanges" "REF"       "ALT"       "QUAL"      "FILTER"    "INFO" [7] "GENO" > lapply(scn[[1]], length) $rowRanges [1] 413361 $REF [1] 413361 $ALT [1] 413361 $QUAL [1] 4 ...
written 3.5 years ago by Miss Agnieszka Aleksandra Golicz40
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readVcf shape of 'skeleton' is not compatible with 'NROW(flesh)'
... Hello, I have a piece of code that have worked on three vcf files but failed on fourth. For the files the reference, samples and gff3 files are the same, only SNP calling algorithm is different. The error I'm getting is: Error in relist(v, part) :   shape of 'skeleton' is not compatible with 'NRO ...
variantannotation written 3.5 years ago by Miss Agnieszka Aleksandra Golicz40 • updated 3.5 years ago by Valerie Obenchain ♦♦ 6.7k
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Comment: C: predictCoding error DNAStringSet_translate
... I can confirm that the code works on the full data set. Thanks for the fix! Agnieszka ...
written 3.7 years ago by Miss Agnieszka Aleksandra Golicz40
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Comment: C: predictCoding error DNAStringSet_translate
... Thanks again. I understand that the fixes are in the devel version of VariantAnnotation. I will have to wait for my admin to install R-devel and will try it out. ...
written 3.7 years ago by Miss Agnieszka Aleksandra Golicz40
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Comment: C: predictCoding error DNAStringSet_translate
... For the future could you tell me how to remove problematic lines. I tried: invalid <- c(123) vcf2 <- vcf[!invalid], but this did not seem to work. Agnieszka ...
written 3.7 years ago by Miss Agnieszka Aleksandra Golicz40

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