User: anamaria

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anamaria40
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Posts by anamaria

<prev • 36 results • page 1 of 4 • next >
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Comment: C: How do you rbind two data frames with a different number of columns without loos
... Thank you so much, this worked great! ...
written just now by anamaria40
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How do you rbind two data frames with a different number of columns without loosing rownames?
... Hi, I have two data frames: > head(df2) ILMN_1658176 ILMN_1794782 ILMN_2329927 ILMN_2338268 DwoC_2318_norm 4.895369 7.354273 5.788415 4.732194 DwoC_3395_norm 4.769932 6.718184 5.338058 4.680381 DwoC_6154_norm 4.944610 ...
R written 18 hours ago by anamaria40 • updated 18 hours ago by RamRS22k
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Comment: C: How to run removeBatchEffect function?
... Hi, thanks. I did run it like this: y <- removeBatchEffect(v, covariate=design) This gives me a matrix of residuals, correct? Ana ...
written 20 hours ago by anamaria40
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How to run removeBatchEffect function?
... Hi, I have design matrix which looks like this: > head(design) (Intercept) SMTSISCH SMRIN AGE SV1 SV2 SV3 GTEX-1122O 1 1363 10.0 64 0.01910439 -0.06545069 -0.01824558 GTEX-11EM3 1 1143 10.0 21 -0.04396299 0.016 ...
removebatcheffect limma written 23 hours ago by anamaria40 • updated 21 hours ago by andrew.j.skelton735.7k
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Comment: C: How do do MDS plot in R?
... can you please send me link to that manual? The problem is that I don't know in which format and which transformation I have to apply on my matrix above in order to be ready for plotMDS function. ...
written 4 days ago by anamaria40
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Comment: C: How do do MDS plot in R?
... I didn't do any step. I do have expression data matrix, rows (genes=Illumina IDs) and columns (subjects). There is 30 subjects and around 15000 genes. What do you suggest I do with this matrix to prepare for MDS process? Matrix looks like this: (I can convert Illumina # to gene IDs) > head(a ...
written 4 days ago by anamaria40
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How do do MDS plot in R?
... Hi does anyone have code for plotting MDS plot like this and how my data matix suppose to look like? I would have there 4 clusters. ![enter image description here][1] Thanks Ana [1]: https://imgur.com/IoCpY2Y.jpg ...
R written 4 days ago by anamaria40 • updated 4 days ago by Jean-Karim Heriche19k
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Comment: C: How to replace rownames in one data frame with column in another data frame
... sure I will do the merge function and that will give me Gene column in my original data frame. But then how to transform that merged data frame into matrix where columns would be entries on that Gene column and rows these DwC_#? ...
written 5 days ago by anamaria40
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How to replace rownames in one data frame with column in another data frame
... Hi, I have a dataframe which looks like this: >head(candidate_gene_exprs1) DwC_1026_30mM.1 DwC_1026_30mM.2 DwC_1026_30mM.3 DwC_1026_norm.1 DwC_1026_norm.2 DwC_1026_norm.3 DwC_6009_30mM.1 ILMN_1762337 4.803651 4.531582 4.992943 5.077257 ...
R written 5 days ago by anamaria40 • updated 5 days ago by zx87547.5k
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Comment: C: issue with ifelse statement
... So I did why you posted above and when I do: > dim(aa[aa$new==1,]) [1] 1513 4 > dim(aa[aa$new==2,]) [1] 946 4 while: > dim(aa) [1] 1651 4 why do total count of "1" and "2" exceed to number of entries in this data frame? ...
written 5 days ago by anamaria40

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