User: scanchi

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Posts by scanchi

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Subsetting a tximport object
... Thank you James! ...
written 17 months ago by scanchi0
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Subsetting a tximport object
... I have an tximport object with 628 files. I want to subset to remove some samples and maintain the tximport data structure. str(txi_object) List of 4 $ abundance          : num [1:56928, 1:628] 14.125 0 15.221 12.45 0.765 ...   ..- attr(*, "dimnames")=List of 2   .. ..$ : chr [1:56928] "5S_rRNA" "5 ...
tximport written 17 months ago by scanchi0 • updated 17 months ago by jennietodd1410
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Comment: C: biomaRT getBM error
... Thank you Mike! That fixed the issue.  ...
written 17 months ago by scanchi0
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biomaRT getBM error
... Dear All, I have used this code to query biomart database previously with no error.  mart <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = 'ensembl.org') mart Object of class 'Mart':   Using the EN ...
biomart ensembl getbm written 17 months ago by scanchi0 • updated 17 months ago by Mike Smith3.8k
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Comment: C: enrichGO returning NA
... I am not sure what I could be doing wrong. I have not had any issues previously working with this package. The only difference between the last time and present is that I updated the bioconductor packages to the current version (3.6.0). Is there a way to remove the 'NA' terms when plotting with dotp ...
written 19 months ago by scanchi0
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Comment: C: enrichGO returning NA
... ##The code with the error. condition.control_dge_subset_ego=enrichGO(condition.control_dge_subset$ENTREZID, 'org.Hs.eg.db',ont="BP",pvalueCutoff=0.05,pAdjustMethod="BH") head(condition.control_dge_subset_ego) ID Description GO:0034314 GO:00 ...
written 19 months ago by scanchi0
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Comment: C: enrichGO returning NA
... Thank you for the quick response. Here is the minimal list and code that can reproduce the problem albeit in a different GO term. I apologize for the long list. dput(condition.control_dge_subset) structure(list(ENTREZID = c("10051", "10052", "100526820", "100527963", "10056", "10057", "10059", "10 ...
written 19 months ago by scanchi0
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enrichGO returning NA
... When I run the enrichGO function on a set of DEG, I am getting NA in the 'Description' column for a few GO term ID's. How could I rectify this error ? Or is there a way to skip NA terms when using dotplot for visualization ?  head(condition.control_dge) ENTREZID SYMBOL 6536 SLC6A9 4601 ...
clusterprofiler org.hs.eg.db written 19 months ago by scanchi0 • updated 19 months ago by Guangchuang Yu1.1k
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Comment: C: Clarification regarding analysis with multi-factorial design
... Thank you Aaron for the useful tips. I will re-post if I have any new questions. ...
written 20 months ago by scanchi0
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Answer: A: Clarification regarding analysis with multi-factorial design
... Thank you for the pointers Aaron. I did use the contrast matrix and the specific coef in the topTable call. I have amended my post to reflect that as well. The condition 1 and control are very distinct groups and no significant DGE between the two groups was surprising. The p-value distribution for ...
written 20 months ago by scanchi0

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