User: mschmidt

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mschmidt20
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Posts by mschmidt

<prev • 14 results • page 1 of 2 • next >
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Answer: A: How to perform alignment of nucleotide sequence containing ambiguous bases
... I have found solution finally. For those with similar problem: library(Biostrings) #generate nucleotide substitution matrix for all 15 base letters needs baseOnly = FALSE nsm <- nucleotideSubstitutionMatrix(match = 5, mismatch = -4, baseOnly = FALSE, type = "DNA") s1 <- D ...
written 2 days ago by mschmidt20
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Comment: C: Alignment to reference containing ambiguity code
... Hi Joana, I am looking for similar solution. You are over 2 yrs ahead with that problem. Did you solved it? Can you help? Kind regards, Marcin ...
written 2 days ago by mschmidt20
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Comment: C: How to perform alignment of nucleotide sequence containing ambiguous bases
... Hi! I have expected to obtain sequences with ambiguous positions. I have sequenced amplicons obtained on metagenomic DNA from environmental samples. The PCR was with universal primers targeting conserved regions within phage genome of specific type to amplify sequences from various virus species. Th ...
written 2 days ago by mschmidt20
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Comment: C: Calculate distance matrix from nucleotide alignment with multiple IUPAC ambiguit
... Hi Denis, I look for solution of similar problem [my_question][1]. Can you give me an advice, do you have solution? Best regards, Marcin [1]: https://www.biostars.org/p/439605/ ...
written 3 days ago by mschmidt20
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How to perform alignment of nucleotide sequence containing ambiguous bases
... I have sequences obtained by Sanger sequencing on metagenomic DNA that contain ambiguous bases (due to amplification of two or more highly homologous sequences). I want to look up for best possible matches from database. BLAST finds matches but treats ambiguous bases as mismatch. I plan to take th ...
nucleotide R sequence alignment written 3 days ago by mschmidt20
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Comment: C: PCA plot from read count matrix from RNA-Seq
... Dear Kevin, all the problems I had was probably because rlog needs DESeqDataSet (`rlog(dds)`), and I tried to generate dds from the TPM matrix which I multiplied by 1e+6. This produced too high counts making the error. Thank you very much for your help! Best regards, Marcin ...
written 10 months ago by mschmidt20
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Comment: C: PCA plot from read count matrix from RNA-Seq
... > str(data4pca) 'data.frame': 45946 obs. of 13 variables: $ bone.marrow : num 6.00e+05 0.00 8.70e+07 3.00e+06 6.00e+06 3.08e+08 1.00e+06 3.80e+07 2.50e+07 4.50e+07 ... $ colon : num 6.5e+07 1.0e+06 8.3e+07 1.1e+07 3.0e+06 6.0e+06 6.1e+07 8.5e+07 2.4e ...
written 12 months ago by mschmidt20
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Comment: C: PCA plot from read count matrix from RNA-Seq
... Your package (PCAtools) has no rlog > log.data4pca = rlog(data.matrix(data4pca)) Error in rlog(data.matrix(data4pca)) : could not find function "rlog" with loaded DESeq2 > log.data4pca = rlog(data.matrix(data4pca)) converting counts to integer mode Error in validObject(. ...
written 12 months ago by mschmidt20
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Comment: C: PCA plot from read count matrix from RNA-Seq
... Hi Kevin, I am using your package (PCAtools). My problem is that I can't get the data **rlog**-transformed. Simple log transformation works, but rlog not. ...
written 12 months ago by mschmidt20
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Comment: C: PCA plot from read count matrix from RNA-Seq
... I want to explore RNAseq data from Expression Atlas (EMBL-EBI database) to get an impression on the similarity/differences of RNA-sequencing samples, i.e. to identify subgroups or outliers. The dataset downloaded from the database was in TPM, so I changed NAs into '0's and multiplied the values by 1 ...
written 12 months ago by mschmidt20

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