User: sjmonkley

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sjmonkley20
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New User
Location:
Sweden
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1 year, 2 months ago
Joined:
2 years, 1 month ago
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Posts by sjmonkley

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Help inputing sailfish TPM files into tximport
... OK after speaking to the people who ran the pipeline I realised I could get the quant.sf files and have done so  However despite setting directory and files as in vignette and these having correct path etc I still get the error (below- there are actually 26 samples but only showed first 6) > a ...
written 16 months ago by sjmonkley20
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Answer: A: Help inputing sailfish TPM files into tximport
... Thanks Michael/Rob as I don't do the Sailfish processing myself as it is part of an in-house pipeline getting the data reprocessed will take longer than I though it would take to reorganize the files. Am thinking not now! When I said the Sailfish output I have has been combined- I meant into 1 dat ...
written 16 months ago by sjmonkley20
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Help inputing sailfish TPM files into tximport
... Hi  I am trying to run tximport on transcript TPM files from sailfish. This problem is that my files are not organised as they are in the Vignette with the quant.sf file for each sample in a separate folder. Instead they had all been combined into one file with separate column for sample. I have m ...
sailfish tximport written 16 months ago by sjmonkley20
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Answer: A: annotating gene for transcript type/biotype
... Hi all First can I say thank you all so much for all the effort you have all gone to on my behalf. I have to admit that with my limited level of understanding of annotation databases I did not follow all the explanations/suggestions given but I got the gist of it. I approached the problem as I did ...
written 2.0 years ago by sjmonkley20
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annotating gene for transcript type/biotype
... I am trying to annotate a table of genes with transcript type (TXTYPE) using Homo.sapiens annotation package within Annotation.Dbi . I want to do this so I can select for only rotein coding genes and remove all the RNA encoding and psuedogenes I m using the following code: all_genes$TxType <- m ...
annotation homo.sapiens written 2.0 years ago by sjmonkley20
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(Closed) annotating gene for transcript type/biotype
... I am trying to annotate a table of genes with transcript type (TXTYPE) using Homo.sapiens annotation package within Annotation.Dbi . I want to do this so I can select for only rotein coding genes and remove all the RNA encoding and psuedogenes I m using the following code: all_genes$TxType <- m ...
annotation homo.sapiens written 2.0 years ago by sjmonkley20
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Comment: C: Validity of using rlog transformed counts (rld) to obtain a list of expressed ge
... Thanks for your very helpful reply. I have 22 samples containing 3-5 distinct cell types- I would like to use this approach to help tell me how distinct. While I agree this is nothing compared to the Barcode dataset I still feel that there is value in coming up with gene lists that are considered on ...
written 2.1 years ago by sjmonkley20
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Validity of using rlog transformed counts (rld) to obtain a list of expressed genes
... Dear Expert(s) (Sorry if this information is provided elsewhere- i have looked high and low with no success) I have a RNASeq data set of 22 samples that can be compared to one another  in a number of different combinations. Some of the samples are essentially treatment subsets of others.  I have u ...
deseq2 rlog written 2.1 years ago by sjmonkley20 • updated 2.1 years ago by Michael Love14k
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Answer: A: Can't load package "org.Hs.eg.db"
... Thanks for sticking with it Dan. Not sure which step worked but it appears to have loaded now. It may have been the above command you suggested although it had appeared to download with other but in the wrong location (complicated by using projects in RStudio with different working directory).  Any ...
written 2.1 years ago by sjmonkley20
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Answer: A: Can't load package "org.Hs.eg.db"
... Dan are you saying that the below should work instead? > install.packages("org.Hs.eg.db", repos="http://bioconductor.org/packages/3.2/data/annotation") When I use it it throws up all sorts of errors and AnnotationDbi disappears. It also freezes RStudio!! Time to give up I think Thanks anyway ...
written 2.1 years ago by sjmonkley20

Latest awards to sjmonkley

Popular Question 19 months ago, created a question with more than 1,000 views. For Can't load package "org.Hs.eg.db"
Supporter 19 months ago, voted at least 25 times.

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